I managed to find a solution on ProtonDB that fixed all my problems, I actually played through most of the game on the Deck already so I can confirm that it works!
I tried it yeah, the language remained unchanged though, my installscript.vdf looks like this:
I also noticed that the unchanged installscript.vdf on my install folder also had
in the "HKEY_CURRENT_USER\\SOFTWARE\\Ubisoft\\Beyond Good & Evil"...
As of Proton 7.0-2 Beyond Good & Evil runs almost flawlessly on the Deck, apart from some sporadic graphical glitches here and there, but unfortunately the default dialog language is french, which can only be changed in the game settings window, which when opened throws the following...