Wow, Andy. Unless the transmitter changes where in the output sequence the sticks go based on mode, there definitely would be a change in operation. If the OP changes from Mode 1 to Mode 2 he needs to make sure that moving the left-hand stick moves the throttle and the right-hand stick moves the elevator for the FlySky T6. If it doesn't, he needs to swap those outputs at the receiver.

Whew, I just looked up the manual and the stick mode does change the mapping as long as the user makes sure the mode is correct.