Luck has it (looking on the bright side of having a hole that is) that the hole is the only one. In that it came from the inside out. The others all appear to the eye to be surface rust. A bit of scraping reveals clean shiny metal. Phew ! Temporarily touched them up with Hammerite just for a few days/ weeks.
I plan getting a patch welded over the hole. I have squirted as much Jenolite fluid into the area as was practical this morning it is dripping out and drying up. In theory that should toughen up the interior around that spot for now. I held off on the Waxoyl as if welding is to take place I don't want it catching fire/causing problems for the welding guy. The hole is 2cms by 1cm on the sill ledge that is horizontal to the ground. (This is pic is just before I broke through it with the screwdriver so it is a bit bigger than this shows)

I am going to the local garage to show them the hole and get them to patch it.
I spoke to Ian from the forum fearing initially thinking that the sill might need replacing but it seems that might probably won't be required. He mentioned around that area there is an air con compressor and this can remain damp and that it is likely that it was used in humid conditions in Japan and this can be a weak spot for rust in the sill. So with this knowledge maybe check yours out asap.
I plan to get the hole welded and then go along the sill and sand it down Kurust it and then either Hammerite or POR15 it along.
So, I am disappointed for all my efforts keeping an eye on things that it has a hole but in reality there is nothing I could really do anyway given it was eaten through from the inside out. Fairly sure that all the other spots are just surface rust spots on the outside.
And to the point...
Once the hole is welded I want to get Waxoyl in but the drivers side of the Bongo does not have any grommet holes to get it in the sill (the passenger side does). So is the only option drilling 3mm holes in and then filling them after spraying a tonne of waxoyl in ? I cannot seem to find any other rubber blanking grommets than about 10mm in size. I do not really want to drill holes of that size in the sill if I can help it. After all how is a hole like that any less of an MOT fail than a rust hole ?