Some of the Greek New Testament manuscripts we possess contain a textual variant when it comes to the Greek word that is translated as "who" (who was revealed in the flesh) and the Greek word for "God." It seems likely for a number of reasons that the pronoun "who" is the original word in the original autographs penned by the Apostle Paul.
It would have been tempting for a scribe who held to a high Christology, one who acknowledged Jesus Christ's full divinity, to change the word "who" for the "God" in emphasizing Christ's divinity. First of all, His deity is not the main aspect of the text in question. Secondly, the use of the pronoun is perfectly consistent with the manner in which Paul writes elsewhere in regard to Christ (Colossians 1:15; Philippians 2:5-11).
Nonetheless, 1 Timothy 3:16 supports the deity of Christ in a subtle fashion. The language of "he was manifested in the flesh" suggests that He existed prior to His incarnation. He was not created, but took on human flesh. This text reflects a primitive Christian hymnal.
The phrase "justified in the Spirit" refers to Christ resurrecting bodily from the grave (Romans 1:4; Ephesians 1:19-23). The phrase "seen of angels" points to Christ ascending into heaven (Acts 1:9-11). The phrase "proclaimed among the nations" refers to His glory being revealed by the Holy Spirit through the gospel to the world (1 Corinthians 15:1-6; 2 Corinthians 4:2-4). The phrase "taken up in glory" refers to Christ being exalted at the right hand of the Father (Acts 7:56-60). Jesus Christ is God incarnate. This note is also insightful as to how 1 Timothy 3:16 points to Christ's divinity:
"Notably, the phrase “great indeed, is the mystery of godliness” may intentionally echo the phrase frequently heard in Ephesus: “Great is Artemis of the Ephesians” (Acts 19:28). If so, Paul is indirectly subverting the cult of Artemis, Ephesus’ patron goddess."