Nope, I think you got it...
Although it doesn't make sense based on what I've seen. Eagle seems to have two layers: 44 (Drill), and 45 (Holes). According to something I read, 44 is for vias (plated through holes), and 45 is for mounting holes (i.e. non-plated). The default Excellon CAM job seems to dump both into a ".drd" file, so I can't tell that there is any sort of differentiation between plated through holes and non-plated.
I wish there was some way to confirm what I actually have. I tried to use EagleUp and when I look at the results, the milling hole isn't showing up, the holes aren't through-plated, and the bottom side doesn't seem to be plated. But another milling hole on the board and vias seem to have it. Now its possible, the lack of through-hole plating is because mine are on Hole layer instead of Drill layer (no idea how to change that), but that may not actually make a difference at the board level. This is very frustrating.