Yes, you are correct, once you go with an MVS setup, whether its a full cabinet or a MVS board attached to a Super NOVA or HGA, you have only MVS settings to modify. However, MVS almost always has difficulty settings, and blood on/off if appropriate (fighting game), and sometimes addtional settings like hidden stages (MSX). The MVS board has dip switches that also allow for interesting changes. The home cart system, on the other hand, may have music selection screen (to play different music tracks) and other options not found in the MVS options.
So, once you go with an MVS setup, you lose home system options, but difficulty is usually part of the MVS setup screens.
I don't think that Jeff modifies MVS setups to include the home system BIOS . . . but I may be wrong. He does, obviously, modify home systems to include the arcade BIOS options . . . a mod I had done and am very happy with!!