I've got the identical setup, 2520 MV, shallow notch transom, battery boxes set up the same way. I have no holes in the location you show in the photos and I have never seen any water in either side box over 19 years of ownership.
Maybe the washdown pump or hose connections in your Port side battery compartment leaked at some point and shed water into that side box and that may have prompted your Dad to drill holes to drain to the deck.
There really isn't any way water should show up in the Stbd side battery compartment.
With holes now drilled in the side of the compartments flush at the deck level, it would be hard to keep water out. I would recommend sealing them up.