For ControlSchemes remove (or move to another location) any file that ends with .binds, then in the Options/Bindings directory rename your current .binds to .binds.backup.With ' blank preset' you mean that you have completely emptied your Control Schemes folder and it remained empty after that? Control Schemes folder being:
What content do you have in your bindings folder /home/<username>/ed-wine/drive_c/users/<username>/Local Settings/Application Data/Frontier Developments/Elite Dangerous/Options/Bindings ?
After that start the game and it should give you a completely blank preset to start binding yourself from, and without loading any conflicting bindings from the control schemes folder.
The issue from my perspective appears to be that when the game scans all the binds including premade ones, it tries to set more than one which locks you out. It may be a particular bind file causing it but I haven't experimented.