Those are playlists, not platforms, unless you specifically unchecked those boxes when you imported Arcade they have always been there, are you still using the same view in the dropdown above your systems.
Pinball FX 3 is a game it is not a system or a emulator, so it is added to launchbox like any Windows game is. You can add the tables and launch them directly, but you need a cabinet code from the game devs. So its totally doable if you want to put the effort in. Unfortunately your lack of patience in setting your pinball programs up are not the fault of Launchbox, we have many many users using them just fine in Launchbox.