The Passagemaker manual doesn't mention this, either, as best I can tell.  We waited until the fiberglass cloth had cured before knocking out the tab holes in the fiberglass which, if memory serves, was not difficult.  Cleaned up with various files.

Yes, you'll want to make sure you work some thickened epoxy into the holes as you're assembling the bulkheads, but don't get so carried away with it that you squeeze great blobs of it out onto the outside of the bottom.  Once you flip the boat over to do the bottom, you're going to saw the protuding tabs off, which'll give you an opportunity to fill any remaining gaps.

.....Michael

Ha!  We've been over this before somewhere in the distant past.  While the tabs are a great for alignment, they do pose a small challenge at this stage of the build.  I believe you can just cut them back out after glassing the cured interior with a razor knife.

At this point, haven't you already glassed the bottom?  So tabs shouldn't protrude.  You can trim the tabs if needed also.

When setting the bulkheads in place, Gramps is correct.  Also, fillets should cover the joint.

 Thanks All!  Exactly the info I needed.

According to the manual, interior should be glassed before the exterior.  Will trim the tabs before glassing the exterior.

That's weird.  My manual is only about 5 years old and it clearly has you tack, fillet and glass the bottom exterior while the boat is upside down on the sawhorses.  I remember because it's MUCH easier to glass the exterior.  That way, you have practice once you flip the boat and do the interior.  Hmmm...  Possibly an update to the manual?