From everything I have read on the subject of body filler, none of it is waterproof, and dura glas is as close to water proof as you can get.
Lets use a floor pan as an example.
Floor pan supports are spot welded to the pan, and there is small gaps in between and around the spot welds.
Lets say you sand, wire brush or sand or bead or whatever, blast the pans and supports.
A lot, or the majority of 40 year old pans and supports are pock marked and pitted.
So some body filler here on our bare metal, if you want them perfect, you will need to get that filler at the edge of those supports, and a little bit under the edge.
If you spray like an epoxy for example, you can get that epoxy under that flange fairly good, if not by spraying, with a short bristle brush you can dab it in there lightly.
Back to the filler, without epoxy under it, if you force the filler under those gaps, you still can't get it in there like a liguid epoxy. If you only use filler, you will probably loose that factory gap.
I also agree with the filler over bare metal, if it's put on right, it will last forever?
If there isn't a lot of difference in the adhesion, between filler to metal or filler to epoxy, which I think is a wash.
Then I would think, bare metal, epoxy and then filler would be the best protection in this case.
Rob