John Gill's Exposition of 1 Timothy 3:16 ("God was manifest in the flesh")

God was manifest in the flesh; not God essentially considered, or Deity in the abstract, but personally; and not the first nor the third Person; for of neither of them can this or the following things be said; but the second Person, the Word, or Son of God; see 1 John 3:8 who existed as a divine Person, and as a distinct one from the Father and Spirit, before his incarnation; and which is a proof of his true and proper deity: the Son of God in his divine nature is equally invisible as the Father, but became manifest by the assumption of human nature in a corporeal way, so as to be seen, heard, and felt: and by "flesh" is meant, not that part of the body only, which bears that name, nor the whole body only, but the whole human nature, consisting of a true body and a reasonable soul; so called, partly to denote the frailty of it, and to show that it was not a person, but a nature, Christ assumed; and the clause is added, not so much to distinguish this manifestation of Christ from a spiritual manifestation of him to his people, as in distinction from all other manifestations of him in the Old Testament, in an human form for a time, and in the cloud, both in the tabernacle and temple. This clause is a very apt and full interpretation of the word "Moriah", the name of the mount in which Jehovah would manifest himself, and be seen, Genesis 22:2.