Infinite Flight does not have access to power management of your ipad - IOS manages both charging and processor temps, and infinite flight just tries to squeeze as much performance for itself as it could. It should probably get better with 21.1 - they needed to optimize the engine to get a few million spare polygons for the terminals, so it’s probably safe to say the atmosphere part of the game is now more efficient, which is probably the only thing you see on cruise.
With that said, batteries do warm up when you charge them - apple can’t defy laws of physics (yet?) - which, coupled with the heat from CPU/GPU can heat up the thermals to the point that the system would throttle your charging. Only thing you can do is make sure you don’t have any background processes running and that the brightness of your display is set to low. Also, if you’re not using the charger that came with your ipad, make sure it is at least 10W.