How to maintain Authoritative / CRC compliant when your server setup makes you fail it?

Hello all,
I am pretty new to networking, so I don't know many (any) tips, tricks, or best practices yet but I am trying to make sure I maintain Authoritative movement in my game, as it is a small online RPG. The issue I am running into is that I just implemented the Master Server Framework (which is fantastic by the way, and free!) but the problem is because of the fact that in order to have your scene interact with the master server or the instance spawners you have to add networked scripts to your scene which basically then allow communication between your game and the master server / database. I have two difference scenes for my game that I maintain via 2 separate projects that are nearly a clone of each other, but of course one is client and the other is server. So while both of my game scenes for server and client are named "_Game", they have and require different things within them.

The server scene has uMMO in it to handle and maintain the connection for the most part once the players are actually in the game, but on then the server side has additional scripts from the Master Server Framework that allow the server to become an instantiated entity whenever it is needed, so the client "_Game" scene does not match up to the servers and I lose my Authoritative movement.

Does anyone have any recommendations on how to overcome this? Do I just need to rig it up and add some additional yet useless networked things to the client side to try and even out the script number? That just sounds silly and not a good use of resources. : /

If anyone has any input, I would greatly appreciate it!
Thanks,