Yep I will fill the tiny holes made by the wood screws they screwed the plywood down with using Tiger seal or similar after I have cleaned up and treated each hole but for the bigger holes i.e where the Unwins track was, that I will not be keeping, or the even bigger holes where the tail lift, patient seats oxygen bottle brackets etc were fitted, I will probably use bolts and Tigerseal. and then underseal everything so it at least matches!
I just happen to have loads of salvaged bolts from caravan floors when I dismantled a couple to build Chicken coops and they have nice flat heads as well so will not protrude excessively inside the van I don't think I need to go to the extent of welding though.
It rather reminds me of an Engineer I worked with at GEC in 1976 who had a Austin Cambridge, every time it failed the MOT for rust he would bolt in a bit of angle iron then weld it up!