Looking at some of your photos, I'd forgotten how much of the holes were taped from the underside. If you were stripping the old sound deadener and the primer to bare metal from your car, I would just tape the inside of the holes - after all, a bit of sound deadener around the hole is not a problem when it isn't meant to be a waterproof grommet seal, just enough to protect the hoses and cables passing through.
When I began to strip the old primer and sound deadener on my rebuild, I realised there was no rust under them so decided to leave the original in place.
The biggest lesson I've learnt from my current restoration is to make sure you use a good metal primer under every other coating. My paint supplier didn't tell me that until I asked. Without the good metal primer, i was getting rust marks coming through the thin edges of the top coat.
Also make sure you know if your spray "sound deadener" or spray "stone guard" will accept a colour topcoat. On minis the underside is not topcoated but the wheel arches are colourcoated. Apologies if you know this already, but noone told me when I needed to know ...
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