So, I've installed GTA via steam and i did noticed battleye which shows the errors when loading the online version

Would this mean until there is a solution, am I thinking the only way to play online is to uninstall the LSPDFR files and then re-install them when wanting to play it?

If you want to play both modded GTA and GTA:O, I'd just create a second directory and keep one unmodded. You just rename whichever you want to use to the original name and keep the other one something like [YOURGTAFOLDERNAME] - Modded. That way you don't have to bother with removing and adding stuff depending on what you want to play.