I agree with a lot you said. currently I have been setting up my retroarch mame 2003 plus cores provided by wiimpathy. His cores are A thru G and v0.4. and i have retroarch 1.7.7 nightly build. for the most part wiimpathy's cores work great as wiiflow plugins but there are a couple i had issues with.
core E - the konami core. Large games 1MB or greater wouldn't work (cowboys of moo mesa, TMNT, TMNT 2, bucky o'hare). Wiimpathy included the v0.3 cores as alternatives so i tried core E v0.3 and those large konami games worked but oddly enuff the games smaller than 1MB didn't. so I created a new core H and put v0.3 and the large games there.
core C - the williams core. v0.4 wouldn't work for joust and defender so I tried v0.3 and now core c works fine for all those games.
I downloaded his capcom core and made it core K. works great for bionic commando, black tiger, ghosts and goblins to name a few.
for some reason I'm having trouble with asteroids and asteroids deluxe. don't know if that's because they are vector games or i have to try a different core. I might use mame 2000 for those games.
As for retroarch cfg versions:
I'm using retroarch 1.7.7. wiimpathy's cores are 1.7.6 and the capcom core is 1.7.5.
Wiimpathy explains here -
https://gbatemp.net/threads/wiiflow-lite.422685/page-87#post-8748088 how to hexedit each core to change the name of retroarch.cfg so that each core will use its own retroarch.cfg. I'm going to do this next even though i haven't had any major issues with them all using retroarch.cfg 1.7.7.