i never really post so apologies if this is a weird read, but i see a lot of other people having the exact same struggles I was having. Worse yet, a lot of the threads with solutions are Windows-oriented, which doesn't really help people who are on Linux.
It's possible I simply missed a thread, but after a couple hours total of ramming my head into the wall, I would like to share what I eventually figured out in hopes that it helps others.

For context, i'm using an X56 Rhino HOTAS system [throttle+stick] on a Bazzite machine, but I don't think the model matters, so long as the external tool supports it. The game naturally detects it, however, the controls are all janked up - most notably, my Yaw control made me look up and down, which rendered my flight stick practically unusable since it's easy to accidentally trigger yaw rotation when the dogfight gets intense. Going from "missiles locked" to "looking at my crotch" was not conducive to good mission performance.

I started by nabbing a controller remapping software off of Github: Joystick-Mapper (don't know how steam forums care for github links but it's published by 'Alphonsvds').
I have this downloaded as a .AppImage - note that it has to be running to emulate the controller.

The software is straightforward and took my control remaps successfully, but the raw input was still bleeding through and producing things like double-taps when scrolling menus and the original incorrect inputs (my Yaw control still made me look up and down while also yawing my plane left/right?)

turns out you can disable that as follows:

• Open ProtonTricks
  
• Open the entry for AC8
  
• click "Select the Default Wine Prefix"
  
• Supposedly, there's a "control panel" option here, but I didn't have it - I instead used "Run a commandline shell (for debugging)", then, in the terminal window, ran 'wine control'.
  
• New window pops up with an option for "Game Controllers" - click that.
  
• Find and disable the HOTAS devices bleeding input through
  
• Close all of the ProtonTricks windows and re-attempt to launch the game, with Joystick-Mapper running

Now that I have done that, game appears to be accepting my inputs just fine. Hours later, i can finally actually play the damn game.
ridiculous for them to not have proper HOTAS support on a flight game. At least let me map my own controls. Gimmie a .ini file or something, man. wtf.

inb4 I go to run one of my games with proper HOTAS support, only to find that I've somehow accidentally disabled my controls for those lmao.