Yes sure you can!
Just type “Retroarch -help” in the command prompt and it’ll show all the options.
So for example loading a core with a specific config file and game you would start the following when in the the retroarch folder (example snes game):
Retroarch.exe -L "cores\mesen-s_libretro.dll" -c "config\mesen-s_libretro.cfg" "path\to\game.rom"
Mind you there is a learning curve with RA, one thing to remember is to enable save config on exit when in Retroarch and it’ll update the config with your setting changes such that it gets loaded again with the changed options next time.
I’m using Launchbox myself and can really recommend it as it makes managing your games library and various emulators much easier. Once properly setup you can even right click on games and choose by which emulator the game should be started. It also automates the proces of automatically downloading game Box images from the Launchbox database when “importing” games etc.
For getting to grips with the core options for the more “complicated” systems it’s best to visit the specific libretro git repository which many of them have extensive README.md if you scroll down. Like te one I linked for Dosbox-pure. If you would like to try the PUAE core a good starting point is the https://github.com/libretro/libretro-uae page, which is very extensive in its explanation.