I've searched through the Google archives and have found several
suggestions on filling holes in hardwood floors such as sawdust mixed
with finish and wood filler. Most of the suggestions were for small
cracks or for nail holes so I do not know if they apply to my
situation.

My dad is refinishing our hardwood for us, it thin (about 1.5" wide
and only 3/8" thick) maple. In one of the bedrooms, the previous owner
didn't like the squeaks in the floor and screwed about 30 #8 screws
into the floor. We removed the screws since they looked like crap and
the funny thing is, the floor doesn't squeak any more than it did with
the screws in it. Anyhow, squeaks I am not concerned about. What I am
concerned about is, the large screw holes left in my floor. My dad has
completely sanded the floors down and put on 3 coats of water-based
Verethane, they look fantastic so far, other than the screw holes. He
can't sand the floors down any further due to the thinness of the
wood. He does not want to fill the screw holes as he says that most
likely due to their funnel shape (narrow at the bottom, wide at the
top), that the filler may pop out over time lifting the finish with
it. After searching around on Google, this does seem like a
possibility.

He said he will fill them for me before the fourth coat of Verethane
if I want, but if it's going to pop out like he says in a few years,
I'd rather leave them. They do not look very attractive though.

Thus, my questions are, should I suck it up and just leave all the
screw holes, or get my dad to fill them? If he fills them, should he
use the maple filler from a local hardwood supplier (they say it is
one of the only fillers that actually looks good), or should he mix
the sawdust with the Verethane? I also saw suggestions of using dowels
to plug holes, but I suspect these could also pop out?

Thanks for any suggestions!