The problem is with "StartPreset.start"
Horizons was a single line with the binding name e.g. custom
Odyssey has changed this to four lines, one for each section, General, Ship, Srv, Foot
My workaround at the moment as I'm using renamed customised bindings called Odyssey
is to load Odyssey, start a game and make sure my foot controls are set to use odyssey in the drop down
Then edit the StartPreset.start file to be only 1 line saying Odyssey
Then start Auora. Which then can read the binding file
Oh wow I see, this is very interesting. Also it took me a little bit to understand your explanation (since you called your bindings file the same name as the game

) so just to reiterate for anyone else wondering, I want to write this in an extremely detailed way:
Elite Dangerous Odyssey changed StartPreset.start (C:\Users\<USER>\AppData\Local\Frontier Developments\Elite Dangerous\Options\Bindings\) to use four lines instead of one when identifying which bindings file to load at the start. Each line just tells the game which profile to load for General, Ship, SRV, and On-Foot controls.
Madproforg figured out that if you start the game normally, make sure your binds are set to the profile you want, and then change StartPreset.start to have only one line containing the name of your profile you use, Aurora will load everything correctly. At least in my case, I didn't t even need to restart Aurora in the process, Aurora was open and picked up the new StartPreset.start as soon as I refocused the game, and functioned properly.
Just keep in mind, every time you go into control bindings ingame it will overwrite the StartPreset.start file with the four lines of each profile. However, since Aurora has already loaded the profile once correctly, it will continue functioning properly for the entire duration of the Aurora program running (even if you restart the game).