I have a small project during which I drill hundreds of little holes (the largest of which is 1/8 in.).
Typically, I have always started with this process, then added ornamental carvings/burnings, then done my routering, and finally, my finishing stain/varnish.
I observed that I must spend a lot of time with a nail to work the holes again as they get a but of liquid down them during this last process. Fine by me, part of the point of the coating is protection so a little extra work to preserve that is not an issue. At least this is what I was thinking 10 years ago.
Now however, I'd be willing to bet that the depth and uniformity of the Varathane is not complete or homogeneous in a hole nor will it be consistent across holes.
Masking isn't an option, the holes are too close together, and there isn't really a huge concern about load bearing requirements or precision tolerances (as I mentioned before, I can rework/reopen the hole with a nail), so basically I'm wondering if the protective finish will actually be adequately getting into the holes to actually provide a benefit, or if I'm just better off doing it at the end and knowing that the holes are unfinished.