For one thing, any idea where? This is one of those "it's common knowledge that
they said..." quotes that get cycled around, but every time I've seen it, there's never been a citation of somebody actually saying it.
But whatever, somebody from Guerrilla probably did mention something about air travel systems somewhere not being feasible for the first game. There's always challenges with game development, and they take time to fix or build, if they even can be done at all with the tools you have available at the time. In the case of Aloy gliding or flying, it could be a ton of really complicated hurdles of LOD management and level design and barriers of zone management and lots of other hassles, or it could be something as simple as the AI was designed to not have to look
up when tracking characters due to their cone of vision being 2D instead of 3D, and that would have been a few weeks worth of work of redevelopment and play testing that wasn't in the schedule. (Not saying that's the answer, I assume enemies do track up, just saying that there are tons of these little things that are a nightmare to developers because they built a routine to do X based on the game design being exactly X, then a designer comes around way late into the project and asks, "what about if we also did Y and Z?" Lots of parts of games are cheats and tricks and dumb hacks that only work because you the gamer don't get to ask the magician how they do their tricks.)
Every new project is a chance to rethink things that didn't work out or were too hard to commit to/complete the first time around. GTA 3 had no flight and had distinct loading gates when you crossed bridges; by GTA SA on the same platform, you were flying all over the place and it almost never needed to pause for loading.
Horizon itself does have "flight" in it, just not on purpose. Eventually you will hit a wall that you cannot find a way over, but technical limitations are just problems you don't have a solution for, yet.