In my opinion, this coming from a submarine modeler as well as a builder of targets, the problem of balancing a drydock is two fold. Lengthwise, the dock must be made in sections and and controlled as such, using independent valves( solenoid valves?) and either pumps or pressurized air. The real area of concern, though, is lateral control. This can be a problem because centering and holding the "ship" on center line while "pumping" the dock becomes problematic. I appears that the dock would require independent lateral control as well.
Bear in mind that the set-up of keel blocks in a dock was a very precise affair and was specific to each ship. I think a model would tend to lend itself to flat bottomed vessels rather than, say, a nicely rounded hulled tug.
All this said, it certainly could be done and I would really enjoy seeing it.
I have a U.S. Maritime Commission V-4 tugboat, which I scratch built, and have often toyed with the idea of building a submerging and surfacing Phoenix, with which Which I could tow to the Normandy Beachhead.