Issue: when placing the wave in any location that isn't open air it causes at least one flying mob to spawn above ground, ruining the ability to complete the wave

Version: 1.20.1-4.2.6

All of those gates use the open field algo. They are not intended for use underground.

What spawn algorithm are you using? The open field algorithm (the default one) is not well-equipped to handle gateways that are intended for use underground.

out of the box defaults, it happened to blaze gate, endless blaze gate and hellish fortress gate

I also found that putting a 5x5 chceckerbox of blocks above the gate seems to make them spawn in the arena