I came across one spot of rust on the lower rear section of one sill a couple of months ago. Like you I’d previously had a look inside the sill sections (which were spotless) and treated with waxoil, so was a bit disappointed, but really expected it one day after everything I’ve read and seen on here.
I investigated the rust spot, and like you found a small hole in the outer sill panel. I cut a small window in the panel to have a proper look, and found surface rust on the face of the inner sill, and back surface of the our sill. I then cut a sightly wider section out, and came to a point were the inner sill was no longer rusty, but there was still a film of surface rust on the back of the outer sill panel.
I cleaned up the exposed inner sill, and treated with rust killer. I also injected rust killer, then waxoil as far as I could get it in every direction around to area I’d cut out, in between the inned and outer panels. Lower down on the bottom curve there is actually a small gap between the two so it is possible flood that area. I jacked the front of the car up and warmed the sill with a heater so that the waxoil would run along the length of the panel.
A friend who is currently doing up a midget and into welding, welded a small patch over the repair, which I’m in the process of sorting best I can cosmetically.
I’m under no illusion that there will be some degree of surface rust or maybe worse elsewhere behind the ‘perfect looking’ rear sill panels, and am planning to have both sides fully and professionally replaced some time soon, maybe this autumn time.
I have considered drilling a few small holes through the rear outer sill panel further along, and on the other side to flood the rest of the void between inner and outer panels with rust killer then waxoil to hopefully hold things off until I get down to major surgery.
I love Mk1s and have been really tempted by some very low mileage ‘minters’ that I’ve seen for sale over the years, but would be very guarded at paying a premium price for a totally rust free one , as there is no way of knowing what is going on in the thin void between these two sill panels - until the first rust bubble appears that is!