This is a really short answer:

I use brass washers in this type of scenario which deform to the rim shape and the nipple. This was the recommended type of washer in one of the books I read when learning the subject, possibly Brandt's book or another similar.

The wheels where I have had to do this have built up nicely. Using washers is good anyway as the nipple turns more easily under high tension than it would against the plain rim surface.