Hard to be brief on this one, so please bear with me.
John 3:13 only becomes confusing because of our perspective when reading the Bible. We do not place the recorded events in their proper time in history. So many people today are ignoring the time markers and time texts in the scriptures. The events recorded of Christ's ministry on earth, His death, His resurrection, His ascension, and His judgment upon Jerusalem all occurred in that generation of the first century A.D.
That very special generation when Christ walked on this earth was the "fullness of time" (Gal. 4:4) in which God had determined that His plan of salvation would be fulfilled in Christ (Acts 3:18; 6:14; Rom. 13:8). That His plan of salvation was fulfilled in Christ is proved by the resurrection of Christ which happened in the first century A.D.
His death on the cross changed many things (Heb 7:12), including the way in which God dealt with our bodily death and with the prison of Hades.
"And Enoch walked with God: and he was not; for God took him." (Gen. 5:24, KJV)
"By faith Enoch was translated that he should not see death; and was not found, because God had translated him: for before his translation he had this testimony, that he pleased God." (Heb. 11:15, KJV)
Enoch walked with God; and Enoch pleased God. The English word "translated" is from the Greek "μετετέθη" (metetethē) from Strong's Gr. 3346 "μετατίθημι" (metaththemi) and simply means "I transfer, desert, change." (1) The idea in Heb. 11:5 is that God moved Enoch from one place to another. In order to "translate" or transfer him, God also had to change Enoch's form in the process.
2 Kings 2:1,
"And it came to pass, when the LORD would take up Elijah into heaven by a whirlwind, that Elijah went with Elisha from Gilgal." (KJV)
2 Kings 2:11,
"And it came to pass, as they still went on, and talked, that, behold, there appeared a chariot of fire, and horses of fire, and parted them both asunder; and Elijah went up by a whirlwind into heaven." (KJV)
The word "heaven" is translated differently in Young's as "heavens" and is from the Hebrew "haš šā ma yim." It stems from Strong's Heb. 8064, "הַשָּׁמָ֑יִם." or "shamayim," which is "heaven." (2)
But, which heaven is meant: the heaven of God's abode, or the heavens of the skies where the clouds move and birds fly?
There are 236 occurrences of "haš šā ma yim" and most of them are used for the "heavens" where the stars and the sun and the moon were fixed. (3)
Gen. 1:1, in the INT - "...God created the heavens and the earth..."
Gen. 1:14, in the INT - "...Let there be lights the expanse of the heavens to separate among..."
Gen. 1:30, INT "...every bird of the sky ..."
Gen. 2:4, INT "This is the account of the heavens and earth..."
Gen. 6:7, INT "...and to the birds of the sky..."
Gen. 7:11, INT "... and the floodgates of the sky..."
Ex. 9:22, INT "...your hand toward the sky may fall hail..."
E. 32:13 INT "... your descendants as the stars of the heavens..."
Deu. 4:36, INT "Out of the heavens hear his voice..."
Josh. 10:13, INT "...the sun the middle of the sky..."
There are many more examples, and each are determined from the context of the scriptures. But most of the meanings are the expanse of the air, the sky, and the heavens which God created for the sun, the moon, and the stars.
The sense then of the taking up of Elijah was a movement up from the earth into the sky, which is what Elisha witnessed. Young's Literal Translation is the better sense of the taking up into the heavens of the air and sky.
Then, are we just assuming that Enoch and Elijah were taken into the heaven of God's abode? Yes, I think we have made assumptions that contradict other scriptures.
"No one has seen God at any time. The only begotten [h]Son, who is in the bosom of the Father, He has declared Him." (John 1:18, NKJV).
"Not that anyone has seen the Father, except He who is from God; He has seen the Father." (John 6:46, NKJV)
"But every man in his own order: Christ the firstfruits; afterward they that are Christ's at his coming." (1 Cor. 15:23, KJV)
These verses testify that no one but Christ had seen the Father at that time when Christ was manifested on earth. Christ was the first fruits. Elijah's taking up was a type that foreshadowed Christ's ascension. Being a "type" means similar to; it does not follow that it was exactly the same as the anti-type.
"9 Now when He had spoken these things, while they watched, He was taken up, and a cloud received Him out of their sight. 10 And while they looked steadfastly toward heaven as He went up,..." (Acts 1:9-10, NKJV)
The motion of the taking up was viewed from those standing on earth and looking up into the sky, or "heavens". We know that Christ ascended to the throne of God (Dan. 7:13; Rev. 5:5-7). But, does that meant the Enoch and Elijah were ascended to God's abode when they were taken up?
No. The rest of those who had passed from this life - either by bodily death, or by "translation" - into the next realm had still to wait for Christ to be the first fruits of the resurrection. They had not yet seen the Father. Therefore, those who had passed from this life before His death on the cross were waiting for Christ's "coming" to be taken on into heaven to be with God forever more.
So, then where were they before Christ returned?
And, this is where confusion reigns. Many people today are having trouble recognizing that Christ did return just as He promised those in that same generation in which He was crucified, so today's readers cannot yet understand that those saved who had been waiting in that prison of Hades have already been separated out and taken home to heaven (Matt. 22:1-13; Matt. 25:31-46).
Enoch and Elijah were waiting along with Moses and Joshua and Jacob and Isaac and Abraham for Christ's promised return. Elijah and Moses had appeared to Christ on the Mount of Transfiguration (Matt. 17:1-4). Moses had experienced bodily death, but he and Elijah were waiting in the same place. That place was Paradise in the realm of the dead (Hades).
We get the picture of the realm of Hades in Luke 16 in the case of the rich man who was being tortured in Tartarus which was separated from Paradise (Abrahams' bosom) by a wide chasm, or gulf which no one could cross (Luke 16: 19-31).
Christ went to that prison after His death on the cross (Luke 23:43) to preach to those waiting (1 Pet. 3:19) to tell them the same things He had told his disciples ... that the kingdom was "at hand" (Matt. 4:17). Their time to be released from that prison of Hades was coming soon in that generation, and He wanted those souls to know it.
Enoch and Elijah were still waiting with the rest of those who had died for Christ's return in judgment against Jerusalem and those who had crucified Him in the first century A D. The destruction of that city which had rejected the promised Messiah and had persecuted His saints had been prophesied from old (Ezek. 22:19-22ff; Lev. 26:28-33) and was prophesied again during His ministry on earth (Matt. 22:1-14; 23:13-39; all of Matt. c.24; Matt. 26:64; Luke 21:20-36; Rev. 1:1, 3, Rev. 22:6, 7, 10, 12, 20).
The apostles preached it continually (Rom 13:11-12; 16:20; Phil. 4:5; 2 Thess. 2:2; 1 Pet. 4:7; 2 Pet. 3:10-16; Heb 9:28; 10:25 among many others). Christ held the keys to the gates of Hades (1:18) and the gates of Hades would not prevail against His church (Matt. 16:18).
His assembly, called-out ones, or "church" has been in existence since the first century A.D. and its establishment on the day of Pentecost (Acts 2:40-42). Therefore, Hades has not prevailed, and no longer exists. It was destroyed after Jerusalem was destroyed in A.D. 70 and that is when Christ separated out those sheep in Paradise from the goats in Tartarus, and then threw it into the lake of fire (Rev. 20:12-14).
All the saved who had died or been translated before Christ ascended to our Father were taken home to heaven in A.D. 70. They are now in heaven. All of the those who had died since the cross of Christ, or now die in the Lord are transformed / changed in the twinkling of an eye at our bodily death. That is when we hear our last trump, and are taken home to be with the saved in heaven forever more (1 Thess. 4:13-18; 1 Cor. 15:51-55; Rev. 14:13).
Now, with everything in its proper time, John 3:13 makes sense, and it does not contradict OT scripture. Putting everything in its proper time and place in the record of the scriptures allows us to see the entire picture more clearly.
This also makes it very clear that the so-called Book of Enoch contradicts scripture and is therefore a product of the imagination of men.
There are many more evidences and discussions of the time of Christ's "second" coming and soon return in that same generation of the first century A.D. at my blog ShreddingTheVeil. See The Resurrection in Three Parts here, The Gathering of The Elect here, all ten parts of the series It's Not The End of The World, and many others.
(1) translate - Biblehub
(2) heaven - Biblehub
(3) heavens - Biblehub