Yes, it's quite a common practice to fill areas that you don't want to get epoxy. In the mold all of those areas will actually get filled in with glass and epoxy to create a smooth surface. During the "mold making" process though I needed them plugged for the first step.
If you look at the clay around the edges you'll see that I also use it to see the edges around the flange and make a nice radius or chamfer in the mold. Also gives me a distinct line for part trimming.
Unfortunately my progess has been a little slow. I had a couple of F500 pieces I needed to fix and now I'm cleaning up that mess and making a down draft table for dust collection. Hopefully first parts will be pulled by mid April though. I'll keep everyone posted.