Not sure about all the body to chassis fasteners as mine seem to be fairly secure. I would say that structural wood epoxy would be a stronger fix than another hole for pulled chassis fixings.
I will say that other sources of annoying rattles are the headlight pods, some tape under the retaining ring for the beam unit often helps. Also the outer seat belt release unit fixing bolts (the 17mm ones) are sometimes too long and the body panels vibrates on the bolt tail, you can see if this has been happening and file a bit off the bolt. Profile draft excluder helps reduce rattles on the bonnet panel contact points and the boot lid, as well as helping to keep the boot water tight(ish).
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