Earnest,
I found the parallelism you drew between the Jesus-Thomas dialogue in John 20 and the Jesus-Peter dialogue in the Synoptics (Mark 8//, but especially Matthew 16) quite insightful and enlightening actually. There is a contrast indeed -- in the Synoptics Peter confesses Jesus as Christ (Mark), Son of the living God (Matthew), Christ of God (Luke) without any hard evidence. Hence in Matthew he is blessed, because his faith doesn't derive from material evidence or common opinion (flesh and blood) but from an intimate revelation from the Father (v. 17). Otoh in John Thomas comes to a confession (of possibly higher content, but let's leave it aside at this point) only after he has seen a (literally) "flesh-and-blood" evidence. Consequently who is blessed is not he but those who will come to the same confession without the evidence (cf. 17:20). If this parallelism has any validity (and I see it as quite likely, as the Fourth Gospel very often "responds" to the synoptic tradition in a sort of "contrapunctic" way), it inclines to take "Thomas"' statement as a weighty confession (of Johannine faith of course) rather than a casual expression of surprise.
Perhaps I should have explained a bit more about the "inclusio". It means a reference at the end of a unit (pericope, section, or the entire work) to the beginning. For instance, in the final redaction of Matthew "I am with you (egô meth'humôn) all days till the end of the age" (28:20) seems to echo the Emmanuel reference, interpreted as "God with us" (theos meth'hèmôn, 1:23). I think it is quite possible that at a certain stage of development of the Fourth Gospel (after the addition of the Prologue but before the addition of the first conclusion, chapter 21 and the second conclusion) Thomas' confession (20:28) similarly echoes the Prologue (1:1), but this is not so apparent now because it didn't remain the "last word" of the book so to say.
As I said earlier I don't think the Thomas-Jesus dialogue (or most of the dialogues in the Fourth Gospel for that matter) needs to derive from any "historical" situation, or even earlier tradition. To put things bluntly (but this is absolutely not pejorative in my mind) it can be "just made up". To take another famous example, I don't think the Nicodemus-Jesus dialogue in chapter 3 with its central Greek pun on being born "again / from above" (from the twofold sense of anôthen, which has no equivalent in Aramaic or Hebrew and is quite difficult to translate in most languages) and the misunderstanding which follows and is essential to the argument would have derived from any "real" Palestinian situation.
The Gospel of John certainly looked "heretical" to many in the 2nd century. In fact the earliest attestations of its use are found among Gnostics (Valentinus, Heracleon, Basilides). It made it into the "orthodox" canon (after many editorial additions) in spite of the rejection of its leading Gnostic interpreters because it was loved and treasured by important sections of the early church. The irony is precisely that there is quite a bit of "heresy" in what many "orthodox" Christians celebrate as "the spiritual Gospel".