No problem code wise with extra breakers. This truly is a sad situation. Your original install was far safer and would pass inspection here. Only question i have is why did you not put the panels in the location of disc. to begin with.
I agree; we placed the panels in that corner of the garage because 90% of the branch circuits were going in that direction. Including the washer, dryer, 2nd floor sub panel, 2 AHU's, 2 A/C compressors, ice maker, data rack, dishwasher, microwave, fridge, freezer, HVL, etc. It would have made for quite a bit more lengths of 12/2 to reach the extra 10'-15' over and the exterior wall wasn't nearly as easy to get wires down into. We figured that corner to be the optimal place between points "A" and "B" and didn't think there would be any problems with getting it passed. It just happened to turn into a giant mess and that's why I wanted to post it here and get other's opinions.
Thanks to everyone for their inputs.