Yeah you're right...and I was one of those that complained about that. BOY is my mind going with old age.
I'm trying to picture this...
Throttle Quadrant 1 - Engine 1
Throttle Quadrant 2 - Engine 2
Throttle Quadrant 3 - Engine 3
Throttle Quadrant 4 - Engine 4
Doesn't fit your needs because bomber engines 1 & 2 are on the same side. I understand that part.
But I don't see the problem with using one of the switches on the quad to change to one of the 4 available control modes in the game. And since you can have different assignments for each mode, rearranging the mapping to suit your wants. Something like....
Mode 1- Fighter Mode
Throttle Quadrant 1 - Map to Engine 1
Throttle Quadrant 2 - Map to Engine 2
Mode 2- GV Mode
Mode 3 - Bomber Mode
Throttle Quadrant 1 - Engine 1
Throttle Quadrant 2 - Engine 4
Throttle Quadrant 3 - Engine 2
Throttle Quadrant 4 - Engine 3
Mode 3 now solves your problem of the engines being on the same side and Mode 1 maps correctly for a twin engine or single engine plane.
Am I missing something here?