@dalves Games that do scrolling (eg. Auto Racing, AD&D) will typically expand the left and top border by one tile, making the active area smaller and appear shifted right. Some games (eg. Space Battle, Shark Shark) that don't scroll, expand the left border anyway, for no good reason. PGA Golf, Deadly Discs, and Sub Hunt are examples of games that don't expand the border and should look centred.
Regarding resolution, maybe it's a good idea if the Retropie creators add a default -z1 switch to the default jzIntv command. That way it looks decent out of the box.
Might also be a good idea to add a default --kbdhackfile switch along with a sample keyboard hack file (empty except for some comments), along with the official jzintv keyboard hackfile documentation with the install of Retropie jzIntv