"In" could be "incorporated" as a bone is part of a hand. Yet there is no darkness in Him so "all things" would not include darkness. Or "all things" does include darkness and then "in" means "in His control" as when a tool is held in a hand. Either way it seems that "in" is not as simple as it might appear. To decide what "in" means in this verse must bring in what we mean by "all things". So if "all things" in v35 refer to all things to do with the church, which Jesus has been talking about, then it would be alright for these to be incorporated into Him as part of His body. V35 starts off with the Father loving the Son, a more fundamental prism than merely the church, so "all things" might include more than the church.
Word for word
The word en (ἐν) translated as 'in', has a meaning which is more like 'within' - but without a specific location - this is not the same as a bone is part of a hand.
The term panta (πάντα) also refers to all, not just all things to do with the church, and not even all 'things' in a physical, tangible sense. It is an absolute all, not as 'one' but in its diversity.
To get a better idea of what 'in' means in this instance, we need to also take into account the meaning of cheiri (χειρὶ), which although translated as 'hand' does not mean a part of the body (significantly singular), but an instrument of action. So this 'hand' does not control all things as if they were the tools, but it is the tool itself, through which 'all things' are possible.
He who comes from above is above all; he who is of the earth belongs to the earth, and of the earth he speaks; he who comes from heaven is above all. He bears witness to what he has seen and heard, yet no one receives his testimony; he who receives his testimony sets his seal to this, that God is true. For he whom God has sent utters the words of God, for it is not by measure that he gives the Spirit; the Father loves the Son, and has given all things into his hand. He who believes in the Son has eternal life; he who does not obey the Son shall not see life, but the wrath of God rests upon him. (John 3: 31-36)
Together the phrase 'given all things into his hand' refers to bestowing an unlimited potentiality on the Son - to placing all things within his instrument of action. As a consequence of this father-son relationship with God (in which He loves as agapa (ἀγαπᾷ) - with reason, esteem, and preference) therefore, nothing is impossible or beyond the Son's potential. As for 'darkness' - this, too, is not beyond or outside of his potential as a human being.
This paragraph describes the difference between John the Baptist and Jesus, between the prophet as messenger of God in the Old Testament, to 'prophet' as 'the Son' demonstrated in Jesus. It illustrates the paradigm shift in how a relationship with God should be perceived - from prophets (of which John the Baptist is arguably the last) speaking of physical, tangible experience and bearing witness to what they have seen and heard in material terms, to Jesus speaking of spiritual experience and recognising the love that God has for him, and with that the absolute potentiality available to him.
And to us.