As the cavity is dry and dusty it's probably in your best interest not to disturb the splash plates. I think I would go to the option of tidying up the hole and using a cover plate using screws and sealant. The strengthening ribs on the panel won't help you to get a plate that is completely flush but using a sheet rubber gasket or closed cell sponge will help. It will be covered in carpet anyway. Spraying the inside with rustproofing cavity wax a good idea. Water in here can cause a lot of damage to the A post area. As it attacks from the inside, by the time you notice it the damage is serious.
If in the future you have to remove the splash guards, that is probably the time to do a more permanent repair to the holes, but worth removing the plate now and then to check if all is well.