Well, not so much. The problem seems to be reliably filling the hole and also having it come up and over to cover the via pad a little bit. I was hoping that if wiped flush then the ink would at least come into contact with the inside border of the pad (and maybe a little bit underneath), but that doesn't seem to happen.
Plus it's very hard to tell when you'd really filled the via. So when baked you can end up with a bit of a divet in the via hole and there's no continuity whatsoever. I even tried manually dispensing some solder paste into those botched holes and reflowing via an air gun, but that doesn't work very reliably either.
When it works, it works well. But at the moment all the workflows I've tried tend to degenerate into a complete time sink, and has a 50% success rate.
The technique seems to work well on V1-only boards because you're filling a "cup", where the bottom is cured ink, and then on the 2nd pass the printer will dispense a complete pad over the via, allowing more tolerance for via holes that may not be completely filled. But on milled copper you don't have any of those advantages.
My next approach is tried-and-true 30-mil rivets, with the hope that maybe I can convince the V1 to dispense solder over the the via pads, which will reflow the top of the rivet to the board. I can either manually dispense paste to the bottom pad and use a hot-air gun afterward, or if I'm lucky I could manually dispense and reflow it all at once.
The latter will probably be too tricky so I'll probably end up going with a second reflow with an air station.
Was certainly an educational experience. There's probably not a lot of people trying to mix fabrication technologies as I am, but if anyone else solves this puzzle, I'm all ears, It's a promising way to solve the DIY PCB nightmare that is vias.