A clean, new sheet of MDF is probably uniform in thickness to about .005" or so. But you can't rely on it being flat, as it can warp in different directions simply by moving it around your shop. If it's securely fastened to the machine, then any unevenness should probably be due to the machine frame itself, as MDF is quite flexible and should easily conform to whatever it's mounted too.
Rather than checking how flat the table is, I'd be more concerned with how flat, parallel, and square the linear rails are. If they are flat, then you surface the table and it'll be flat. If the rails aren't parallel to the the table, then it's possible that the table won't be flat, even though your indicator may tell you it is.
It sounds like your MDF table is larger than your machine can reach. If so, you should mount a secondary piece of MDF that the machine can reach completely, and machine that flat.