Although it is by no means optimal that someone should drill out those holes a bit to make it align (letting the vehicle roll and settle is usually enough to get them to lineup) it is likely not critical and you probably do not need to address it further. However others may want weight in as to whether, since these four bolts are the main connecting point of the subframe mount bushing to the frame (whereas the main bolt mounts the subframe mount to the subframe itself), the enlarged opening will compromise the integrity of that connection at all, especially with respect to any lateral movement. I do think that it is probably not significant.
The purpose of the plates is two fold. One is to protect the vehicle in the case of a sub mount failure, the other is to provide a weather seal to prevent corrosion to the critical main subframe bolt. Accordingly, your plate should have a rubberized backing to it. If it does not, you can either replace the plate or clean up the plate and use some rubber inner tube and contact cement to fabricate a two layer replacement. It is indeed a good idea to spray some surface shield in there to prevent rust. Make sure the two small drain holes next to the plates are clear.
Probably good idea to check the status of the actual rubber on the subframe mounts underneath by lifting the car lift the car on each side to separate the subframe from the frame a bit so you can inspect them. But given the presence of those shavings that might be a clue they were replaced at some point already!
Here is an annotated pic from Authentic website showing the rubber backing.
