Most of the guys that I've seen do flat bellies cut out the whole floor, and then frame it in, and reinstall it, and recover the tunnel. This gives the whole bottom of the cab a lot more support than just cutting out and reinstalling the tunnel.
The angle of the transmission with or without a flat belly shouldn't make a huge difference, I've got a feeling its a coincidence. The only reason I could see for that is if you've got some slop in the transmission or in the mating of the transmission to the motor, and t-case to transmission. I'm just guessing on that one. But if you think about it, it shouldn't matter what angle the transmission is at (within reason) it didn't grind when going uphill did it? thats an angle change as well, and a more significant one than doing a flatbelly.
