Since this was originally my thread: in my experience with multiple parties having aarakocra in them since 2018--one of them with two at a time--a flying speed has never been a problem for combat balance. Even in a Dark Sun game that takes place mostly outside, a healthy mixture of flying monsters and monsters with ranged abilities keeps that from being a problem.
It is true that some exploration challenges can be trivialized by flight, but I've found that at low levels, flyers are too fragile to survive significant falling damage. A healthy sense of self-preservation goes a long way towards reining that in. By the time they're durable enough to be doing risky or dangeorus things in the air, it's also around the time your spellcasters get Fly, so you'd have to consider that dimension when designing challenges anyway.
Edit: Also I don't actually have a problem with limiting sustained flight to a few rounds at a time at low levels, but the fact that the paragon gift doesn't eliminate it feels very underwhelming compared to others, such as elves having the option to eliminate range limits of their Darkvision or Planetouched getting immunity to a damage type.