In some mods you can have different settings only for a specific map, etpro has per-map autoexecs for sure
I use this feature only for spawnpoints and spawntimers, so I don't know if graphic settings that require a vid_restart will change, probably yes (but I didn't test it). This way you can change brightness only for 1 map.

As regards nonexisting cvars, obviously if you set some fake cvar in your autoexec, it will go to your config, and it will also be autocompleted with tab like real cvars.
And also if you switch mod without quitting first, all the extra variables from that mod could go to another mod's profile, for example I often find etpro b_ cvars in jaymod, etc. but of course they have no effect there.

And a /cvar_restart will obviously delete them, since they are not real cvars for that mod.

I think the best thing would be to have generic ET cvars in one main autoexec, and mod specific cvars in other mods folder, personally I have almost all the cvars in my config, so even if I do a cvar_restart or I delete my profiles folder next time I start et everything will be again with my own settings.

If you don't know if a cvar exists or not, you can try to find that text inside et.exe and inside mods dll, if you canì't find it then chances are that cvar doesn't exist. Same if you do a cvar_restart and the cvar is not there anymore (doesn't autocomplete, etc.)