I agree with them. Avoid any modifications to your car without consulting your dealer. This may void your warranty unless you want a headache in the future and go with replacing your steering wheel switches.
It sounds like a design issue and you did the right thing insisting to the dealer. I just can't believe that such an extensive repair is needed for a brake light. Talk to your dealer and demand for a loaner car.
That is outrageous. It seems you have been like a ball that;s being tossed around. Aside from the deposit did they try to win you back or offer additional compensation for the hassle?