So I found a consistent method to take pictures of grounded flying Pokemon:
Send out a flying Pokemon (with a standing animation available) using ZR. Then, press the left control stick to make them stand still. Slowly advance to your Pokemon while spamming the A button so that you can interact with them from as far away as possible (so you can ensure your Pokemon are in the picture). Interact with A to make it go into it's standing animation (if it doesn't go for it, press the left stick again, back away a bit and try again. If it lowers but doesn't get on the ground, just keep spamming A until it fully gets on the ground). While it's in the animation, spam the down arrow button (for just regular pictures) or the minus button (to go to the Pokedex, Profile, then Profile Picture) to pull up the camera app. From there, apply a filter or whatever (just don't turn on the music), and take your picture.
There are a couple flaws, most notably being:
-You can't move around in or after you exit the camera app or the Pokemon returns to its flying animation, meaning you can only really take front shots. This means you're also at a set distance to take pictures from.
-If you take too long, the Pokemon might fall asleep.
-Again, the music disrupts the standing animation.
-Some Pokemon (like Roaring Moon and his wide-ass wings) are near impossible to take solo pictures of because you're they'll be too close to the camera for them to show up on it.
Those were the main flaws I could find. If this is good enough for an answer let me know.