Before machining the bottom plate, I updated the CAD model. In the new model the pockets are not that deep as in the initial version of the model.

Why did I change that? Well, there are several reasons. 

1. More weight of the vacuum table. Weight is good for CNC milling machines, but of course, it is not so good for the machinist ;-)
2. Reduced milling time. But for me, it doesn't really matter.
3. Less waste to clean up

In addition to these changes, there are some deep pockets close to the pneumatic connectors, since they are about 10mm thick.