Proton is Valve's Wine integrated into Steam, it's essentially vanilla Wine plus some extra patches (that will eventually work their way upstream) and libraries to make your life easier. You enable windows compatibility for a non-native game and it will run in its own prefix. If you are using Steam for games there is no real reason to use a different build of Wine although you can definitely do so. In fact different custom builds are out in the wild that can plug into Steam and be used alongside the official Valve builds.

I can't see why a third-party program cannot be used with Proton. You can just add it as an external program and enable windows compatibility as you would with a steam game.