Raised area in plywood is a problem - please help
2mm humps are not common with good quality plywood. You could plane or (with effort) sand that flat without impacting strength. (Note that you would impact the finish, as you'd go through the veneer into the inner plies.

MDF would be flatter, but not as strong as plywood. If you need dead flat and a nice finish, (and you had room) you could consider putting a thin skin of mdf (like, 6-12mm) on top of the ply that you'd flattened. (You might even get away with not flattening the ply, as the mdf skin would make the 2mm difference very hard to perceive.)

Alternately, and you'll have to judge if this is appropriate for your application, you could put the hump at the bottom of the bed where it might be less noticeable.