It’s possible on PC at least:
Download and install appropriate version of vJoy from Github.
Download Joystick Gremlin from Github and extract somewhere.
Launch Joystick Gremlin and use the merge axis function from the top menu to merge your toe brake axes into a single axis on the virtual joystick (virtual joystick should be automatically created). In this case you’d want to use the maximum method, which means the virtual axis is monitoring both your toe brakes but automatically drops the input from the one that is being depressed less. Save and activate profile.
Launch MSFS, go to controller options, unbind the brakes from your pedals and then go bind the appropriate axis on the virtual joystick to both of your brakes.
Tada, uniform braking on toe brakes with no software input conflict.
If you still want to use differential braking, you could use Joystick Gremlin to split your stick’s twist axis so that twisting it left reads as one virtual axis and twisting right as another, and then go bind those to your left and right toe brakes.
Alternatively you could try to set automatic proportional reduction of the brake on the opposite side while you are applying your rudder. This is actually how real life planes with unified brake lever (usually on the flight stick) tend to work. That being said while I have a set of pedals without toe brakes I have been using OEM’s software to this effect and haven’t tested it, but it might be possible with just Joystick Gremlin too.