I recommend that the English.SE will be a better place to receive grammatical explanations. The antecedent of "He who" is the mystery of godliness. The reason He has been supplied in the English versions with the relative pronoun is merely for either for smoothness of English or clarification to emphasise that the mystery is Christ. It is a common practice in translation, and sometimes there is necessity to supply words where ellipsis has been used in the Greek.
The argument that "he who" has no predicate was used by 19th century proponents of the Authorised Version to attack the Revised Version. Some argued that the "he who" phrase has neither an antecedent proceeding it to be a relative phrase, nor it has a predicate. The antecedent is clearly "mystery" μυστήριον·, so their argument was that the masculine pronoun cannot be used for the neuter mystery. This is wrong, as the relative subject occasionally takes the gender/case/number of its antecedent or predicate, which is called the rule of attraction. Ex. Col 1:27
what is the riches of the glory of this mystery among the Gentiles, which is Christ in you, the hope of glory. τί τὸ πλοῦτος τῆς δόξης τοῦ μυστηρίου τούτου ἐν τοῖς ἔθνεσιν, ὅ ἐστιν Χριστὸς [some later mss also changes the pronoun to masculine: • ὅς ἐστιν] א (Sinaiticus) C D H I Ψ Byz ς (Textus Receptus)] Textus Receptus also changes the neuter "what" τί τὸ (the riches) to masculine • τίς ὸ] ς
Subject and Predicate:
Pronouns like "Who, He or That" can be a substantive subject of a sentence, and a sentence like "Who/That/It was" can be considered complete. A substantive is a word or a group of words that functions as a noun or noun phrase in a sentence. A substantive clause acts as a noun and can take the place of any noun-role in a sentence, including as a subject. A complete sentence must have a subject and a predicate. Therefore, a sentence like "Who was" or "It is" are complete sentences (in response to a question), with substantives/pronouns serving as the subject and "was/is" as the predicate. Also note, that the name of God means, Rev 1:8 (RV) "I am the Alpha and the Omega, saith the Lord God, which is and which was and which is to come, the Almighty".
Great is the mystery that he was manifested in flesh; Or "Great is the mystery who/which was manifested". For further clarification, simply supply: Great is the mystery, that (it is) he who was manifested. There is nothing incomplete and ungrammatical here.
Since the subject pronoun He was added for clarification in the RV, that reading may have caused the confusion and awkwardness, which is why the modern versions simplified it by removing the relative pronoun "who".
Wallace writes in his Exegetical Syntax, pp. 341-342 about the interpolation of the pronoun in 1 Tim 3:16 to theos/God:
The textual variant θεὸς in the place of ὃς, has been adamantly defended by some scholars, particulary those of the “majority text” school. Not only is such a reading poorly attested,’ but the syntactical argument that “mystery’ (uvotnptov) being a neuter noun, cannot be followed by the masculine pronoun (ὃς) is entirely without weight. As attractive theologically as the reading θεὸς may be, it is spurious. To reject it is not to deny the deity of Christ, of course; it is just to deny any explicit reference in this text.
fn: Young, Intermediate Greek, 76, enlists this text as an example of a gender shift, arguing that “the mystery of godliness” refers to Christ.
fn: In particular, it is impossible to explain the Latin reading of a neuter RP as deriving from θεὸς, showing that ὃς was quite early. Not one firsthand of any Greek witnesses prior to the 8th century read θεὸς. Since θεὸς was a nomen sacrum, it was contracted as OC in the MSS. The possibility thus exists that OC was misread as ΘC in about the fourth century and, owing to its richer theological content, thereby ended up in the vast majority of MSS. (See the discussion in Metzger, Textual Commentary, 641.)
fn: J. W. Burgon, The Revision Revised (London: John Murray, 1883) 426 (cf.also 497-501). Burgon adds: “Such an expression is abhorrent alike to Grammar and to Logic, —is intolerable, in Greek as in English.” Though eloquent in rhetoric, Burgon’s argument is lacking in substance.
The NABRE version mentions in its footnote under this verse:
3:16 Who: the reference is to Christ, who is himself “the mystery of our devotion.” Some predominantly Western manuscripts read “which,” harmonizing the gender of the pronoun with that of the Greek word for mystery; many later (eighth/ninth century on), predominantly Byzantine manuscripts read “God,” possibly for theological reasons.
For those who think the sudden masculine pronoun is unnatural, then I'd suggest following the Western mss variant which has the neuter pronoun for the mystery, that will be more appropriate and remove all problems. It is possible that which was originally the neuter pronoun, was changed to masculine for strengthening the interpretation, which was later changed to God, which is the worst variant. Though scholars argue that it is likely that ὅc be changed to ὅ than ΘC. This neuter pronoun is found in these mss, including many Old Latin Vulgate: • ὃ] D* (061 ᾧ) itar itb itc itd itdem itdiv itf itg itmon ito itx itz vg Ambrosiaster Victorinus-Rome Hilary Severian Pelagius Augustine Theodotus-Ancyra Marius Mercator Quodvultdeus Varimadum (from Laparola apparatus, Variant Readings commentary module).
Ὃς Translated as He
Quote from Mounce, Basics of Bible Greek:
Upon searching for the occurrences where the relative pronoun (G3739 TR he) is translated as "He" using theWord Bible app, we get 25 results in KJV, and 37 for NET.
(KJV) Acts 9:39 Πέτρος συνῆλθεν αὐτοῖς· ὃν παραγενόμενον ἀνήγαγον εἰς τὸ ὑπερῷον Peter arose and went with them. When he was come, they brought him
13:30-31 Ὁ δὲ θεὸς ἤγειρεν αὐτὸν ἐκ νεκρῶν· ὃς ὤφθη ἐπὶ ἡμέρας πλείους τοῖς συναναβᾶσιν
But God raised him from the dead: And he was seen many days of them which came up with him from Galilee