I would be rather surprised if the base wasn't machined flat. The base is, if I recall correctly, sand cast and then machined on the outside, and the sand cast "pebbling" is left alone on the inside. (Someone please correct me if I'm not remembering these details correctly.)
You're pressing down on an "edge" of the turntable, if I understand correctly. Note well that the turntable is attached to the drive base by means of a nut threading onto a stud beneath the center disc on the turntable. However, it is not just the nut being torqued down on the turntable. There are (on mine) two springs between the face of the turntable and the nut. When you tighten down on the nut, you're compressing the springs to apply pressure to the turntable in a way which, I would think, allows one to tune the tension to achieve a desired amount of pressure on the clutch discs, more easily than what could be accomplished than by just tightening down the nut directly against the turntable.
What I'm wondering is if the rocking you're observing in the level vial is a small amount of rocking allowed by the springs. How hard are you pressing on the turntable, would you say? Not in units of weight or anything, but something like firm finger pressure, for example? And, if this is the case, I wouldn't be worrying about this.
I may try to duplicate your issue on mine sometime, but it may not be today. I've got what feels like a real nasty ear infection, I think, and I need to get some attention for it.