So how does the PvP actually work, is it real time pvp or turn based? You should give us more information about the game in your first post and maybe a video demo/trailer of the game to have a better idea.
Actually I have a couple different versions of this game created and I can't decide which is "best".
I personally prefer the Real-time PVP, with skills and tarnishing battle items.
There is also a Turn-Based combat version with no skills or tarnishing battle items.
I will probably be hosting the Real-Time version with skills, because it has my personal bias

Yeah, this is basically my biggest road-block at the moment. I want a universal server, and the game engine also has some security flaws so it might just be better to just re-create the game in a better game-engine.
A universal server for a small game is a big ask. I think you should say ranked games on official server but users can play on their own hosted servers any time they like, most people play for fun at first and a small game doesnt want to discourage people picking it up and starting as soon as possible. WIth so much competition out there you almost instant action if possible

This much is becoming clearer and clearer, and I'll probably just release separate clients for separate servers, with options like you're explaining.
I'd hate to kill myself attempting to link the servers across platforms, vendors and OSes when it wouldn't bring much
more hype to the game.