The issue isn’t that flying would be ground shaking tech - maybe they didn’t think of it, or didn’t think it was a good idea, or it would diverge too much from their D:OS2 formula, after all flying in the air would cancel a big chunk of Larian’s home brew - pushes gone, guaranteed to hit surfaces gone.
The thing is, I feel that a bunch of mechanisms and abilities like Short vs Long Rest, Reaction or Advantage, as well as flying, prepared spells, upcasting spells, stealth/sneaking, classes differentiation and balanced-party-building, ... are all staple features of 5th Edition in particular, or DnD more generally. So, if it is indeed the case that they started working on the engine and then the core code of game only to discover down the line that they have difficulties implementing one of those staple features in their system, then it means they didn't bother reading the manuals even superficially and designing/conceptualising what they would need to be able to do before moving to the developing/implementation phase. (Hopefully, this is not the explanation. But, sadly, my faith in Larian's skill in project management is sufficiently low that, if Swen gave a talk and told us that they starting thinking about how do deal with flying (/Reactions/else) mid-way through the EA, I would not be too surprised.)
Also, Larian made a big deal of verticality in their communication and marketing of the game. I have difficulty reconciling how they could choose to bring so much attention to this aspect and are
delivering so poorly on it.