So you can either have wings and average maneuverability or no wings and perfect maneuverability. Oh, but the second can be stopped by a 6th level spell or 10th level Advanced Technique.
So until 10th/12th level this is a free perfect maneuverability?
Also wouldn't those anti-magic effects likely cause the companion to wink out anyway, due to being summoned?
I'd note about it that.. It seems to change from player to player whether they think things like this are good or bad.
Some say that nonmagical flight of any kind is really useful and that they have saved their party multiple times using it (with the Angel Wings Feat)
Others say that these nonmagical flight options are subdued by other options.
Honestly, the difference in balance probably isn't big enough to worry about. PCs are more-or-less expected to have access to regular flight around level 5 to 6-ish anyway (that's when the Fly spell comes online), and it's constrained by low ceilings in dungeons and the fact that ranged weapons and spells are a thing. Just make sure tough enemies have a way to hit ranged targets and I think you'll be fine.
If you really want to balance them out, perhaps make the magical flight less precise than the mundane one?