I really think that they could have foreshadowed draconification better. It wouldn't even have been that difficult. (rant incoming)
I think my issue with it is that it's specifically brought up as a way to get to the future/present, which just makes it obvious that that's what it's going to be used for. If it was brought up outside of that context, it would have been less obvious.
Zelda is supposed to be the Wise™ one as well, so having her work it out herself could have been a lot more interesting.
Off the top of my head, have Zelda ask Mineru about the relationship between Zonai and dragons, as she's shown to know that they're related in the prologue (if memory serves). Then have the exposition about draconification. Without changing much, this immediately:
2. Hides the twist slightly better
3. Makes Zelda a more active character
Whilst not requiring too much new work to be done (animations etc.)
This is especially infuriating if you remember that memories can be collected out of order
Anyway there are my poorly worded thoughts