I had to cut such holes for access to hardware behind the liner. The thought to make them double as speaker enclosures did occur, but I couldn't find speakers that would actually fit in the available space on my boat.
I cut some access holes for cleats, winches, etc., and installed the Beckson deck plates that have storage bags behind. I found them very useful in the helm area.
Given the difficulty I have had in accessing the backing plates for the stern fittings, perhaps the PO installed those openings to make reinstallation of the fittings much easier when rebedding.
After crawling around my E26, I think the fellow that installed those stanchions and other deck fitting at the factory was short, skinny and had very long arms.
Or it could be that the fellow was normal in size and dexterity but did much of the assembly to the deck before it was bonded to the hull. I removed every piece of hardware and trim for deck painting and I was convinced the assembly had to be done that way. I could be wrong.....