Also, only once did I have to re-map my controls (though this was a 'known' for that current Mame version) and in any case I have a simple set-up that applies to most games. However, I'm not sure affected specific ones that were different from my global settings. For example, an analogous situation is video settings: if I go and specifically set them in a game, and then go and change the global default settings, this game in particular is not affected. I think it happens the same with controls.
Most remapping can be covered by using ctrlr file instead of "input (this game)", and carried to the next version (but there versions that have broken the ctrlr made before then). Heck, even the "input (this game)" (the cfg files) usually can be carried to the next version, but not as reliably. The nice thing about the ctrlr file besides working cross versions is that it can map for all games, special games, a parent and all it's closes, all games that use a bios, and all games within a mame drivers (neogeo games being the most well known).
And yes, if you remap in "input (this game)", that mapping* will over ride any maps in "input (general) and in the ctrlr file, but only the input remapped. (*with one minor exception)
Anyway, what I do is copy my mame.ini file to the new version, run mame -cc to fix it (if any option was removed or added). This way I keep all the rompath and other options I've changed from the default, including the ctrlr file, and after compiling it is nothing. This way all my settings are moved over, but if any setting was removed, I get a warning before I start to play, so I can fix it before I get into the "I must play now" mode.