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When updated through ISTA/P at the dealer, ISTA/P backs up the profile from NBT and restores after programming so your convenience buttons and other settings stay programmed. The backup and restore is not always successful especially if programming is interrupted so that could be what is being observed here.
In terms of 58.2 vs. 58.3, I can't speak to specific differences in every car but going from 58.0 to 58.3 in my 01/16 build car only updated NBT. Older builds have reported additional modules being updated in 58.3 but I have not see conclusive evidence of this.
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