The only thing that matters for level in a shower pan is the top of the threshold where the tile or shower surround will meet up with the pan. If you set the pan in the space that is when and where you check for level. The tiling flange can be wildly out of level because its not visible after finish surfaces are up.
Put the bubble directly over the drain cut out with the topside up. Is it in the center? The pan floor should all sloop to the drain. If not. A base of mort under the pan can do the final level.