I have to tell you, I would have left it alone. My daily driver 59 Rambler as a spot similar to that, the rest of the car is nice, it staying like that. It IS a driver and when people see an old car like ours, they are impressed it's even on the road. When it is largely in nice shape they don't even see that stuff. I have had people ask if I recently restored it thinking it was a work of art and it is FAR from that (brush touches all over it). If you have your passions on that frame off (I have the same thing in my life) I would have left it alone.
However, that isn't a choice now is it. It is so hard to do anything that will last very long at all. But if you use a reinforced filler like Everglass and you spray some cavity wax inside to protect it you are going to be about as good as you can be. I know that I saw a lot of this type of repair when I was a paint rep, up on the north coast of California where the salt air eats car alive. I was in a shop I serviced and he was making "repairs" like this on a school bus. This was not the type of work he generally did and I asked him about this and he said the school district would give him a bus like this every once in a while and he did this funky repair and it kept the bus on the road another year or two. Up there, that is darn impressive so if another year or two is what you are after (damn that year or two goes by fast) then there you have it, Everglass, tap in the holes some what so you have a dent with the hole at the bottom. Treat it just like any other dent you would be filling with filler. But fill over the whole thing with Everglass first. Cut it flat and put a skim coat of polyester putty or regular filler over it, prime and paint and cruise with a smile on your face.