I did read it again, and I don't see a lot of easter eggs. 
Yes, there's the fact that Jude betrayed Joshua and the Great Engineer, and then later felt sorry for it and ended up getting sent to the Fogworks.
But I don't really see any other parallels. No mention of something like thirty pieces of silver, nothing like Judas's kiss, nothing that happened before this to indicate that Joshua knew Jude would betray him the way Jesus did... The only possible connection I see is that the house where the betrayal happens is surrounded by (or near) a garden. But of course, Adam and Eve's sin took place in a garden as well, and the fact that Magda says the Great Engineer supposedly planted the garden in only six days heavily suggests that this is the Garden of Eden.
As for
I don't quite agree. Yes, we've got characters representing people from later in the Bible showing up in episode one, but I feel like this was largely to expand the cast of resistors. For the most part, the Aethasian timeline stays in chronological order, even if they seriously cut down the time between major events.
I'll admit, there isn't a lot of evidence pointing to the Everbrights being Adam and Eve either, but it seems more in line with the timeline. I could be wrong though. (Personally, I think that the Scarlet Man is going to get sent to the Fogworks upon being betrayed, and then three days later, break out. But that's just my theory.)
As for the depth of the Aethasian flood waters... I believe it says in the book that the Aethasian flood only covered certain valleys where they grew most of their crops, so it couldn't have been too big.
