The 2 are unrelated.
Not sure why the bomb was removed but I suspect it was the same reason as on the E-4 -- to represent more of the pure fighter v fighter war of the time.
Gondolas just weren't used on 109Fs. A very small percentage had the proper wing modifications from the factory, and even then that doesn't mean they used them. It was really a testing phase and was used after that (so use the G-2 -- very similar in handling to F4 and the extra speed makes up for the loss in speed when you have gondolas -- making it juts about as fast as the F4 without gondolas)