I think the only bad thing that would happen in the DB601 is excessive engine wear, much like the use of take-off or emergency power for Merlin engine.
The explanation for Gate control comes from:
http://www.enginehistory.org/Piston/...erlinABC.shtml
Agreed about the virtual limitation. It would be the best if take-off boost settings simply wouldn't provide a increased boost above their limiting altitudes. The engine seems to be able to handle this, as can be seen in the speed graphs of Blenheim and Fiat G.50 (I didn't test so far what happens if take-off boost is used above that altitude in these planes).
Alternatively engine damage could be forced above these altitudes, much like the GM-1 restriction from old IL-2. But I guess this would be incorrect in most cases.