You can but it might ackward and have the same issues you might be looking to avoid using the builtin Retroarch override system.
I don't use them anymore, but you can pass Retroarch the location of the Retroarch config file and at the very least have that config put the to a different location for the options file.
Retroarch doc is here.
Not that I know of. You could also use a prelaunch command to copy/modify the options file manually which wouldn't tie it to the name. I have use this in the past but it's cumbersome to maintain (easier using Joe's bulk editors), but I find it was easier just to use the built in options for my sanity rather than trying to remember what hacks/routines I used for specific games.
