Dedicated server based on MasterServer. Can it be done?

I've been researching for a week about networking in Unity. I am more than capable of handling any kind of single player project but when it comes to networking all my skill fails me. :( Anyhow the main question is this. I get it that the dedicated server is software which handles the game logic based and sends data back to the clients. But as I can see the people talking about Unity networking server have no idea that it cannot be done. Hear my example: Both server and client game implementation can be in project filtered by isClient || isServer checkups. However to be actually able to do this, you have to have a created game that is on the same scene as the players (game scene). That means the server is player but doesnt actualy control anything he just handles the game logic for clients. How can i then have multiple games created and people can join them. That means that multiple instances of the game have to be runned on the server. But that's not dedicated server its just masked since you have a bunch of "server players" that create game and clients are filtered. So the actualy question is: As far as i've understood by now the server is software that will be able to handle the game logic for players and I see no way of making this within one Unity project how can you then create such dedicated server if it is even possible.

To be more clear the game system I am aiming at is Dota2 or HoN like where you join a queue and then you get paired with players which i think I'll be able to do, but that client server part just breaks me.

Any help is appreciated, thank you in advance.