After I upload my numbers, if I am missing a player, FC will use the FC default numbers for that player. So I have to make sure I click "Show my Projections" in order to use only the players I uploaded.
Sometimes I forget to do that and I get a FC projection mixed in with my numbers.
I, for one, would like to have that option (show only my projections) as the default option (or at least, like I suggest in the OP, an option under my account setting)
So to clarify, whatever I upload - thats all that would run in a optimization unluss I add some of the FC projections manually.