It definitely is something that you and your plumber have to get together on.
The definition of the toilet rough-in dimension is the distance from the FINISHED wall surface to the center of the toilet mounting flange (measure to the mounting bolt holes.)
So, if the wall is to be finished with one layer of ½" drywall, the plumber would rough in the flange at 12½" from the studs. ( or 10½"). If the wall is to be done in some other material, for example if it were proposed to be tile over a backer, the plumber would have to have this specification.
Now, here's where you come in. You get to choose the toilet. Almost all toilets installed today are 12" rough-in. If you rough at 12, you will have the greatest selection available to you. When would you use 10? Possibly in a small room where a little extra clearance for a door opening will be advantageous. No problem. You can get a good toilet, but some models or styles may not be available to you in 10.