If you know the thickness of your desired flooring, you could lay some sheet goods there, install the flange at that height, and temporarily set the toilet. While not a horrible situation, ideally the flange will sit on the top of the finished floor. Or, if you have access below, you could just set it on the subfloor, and then cut it off and reinstall new when you add the finished flooring. If you plan something like sheet goods (vinyl), then just set it on the subfloor...the thickness of that won't matter, but it could if you were to add a second layer of ply and maybe some cbu, and tile.
Most toilets won't sit properly unless the flange is either on the finished floor, or maybe as low as even...but for the finished thing, on the finished floor is still the way they were designed to fit.