I decided not to use the filter shown above and to allow wordpress to act like wordpress despite creating a lot of 301's on my behalf. If a visitor lands on the right page it's beneficial, imo.
I dealt with the trailing dots with htaccess, is there a more efficient way?
RewriteRule ^(.+)\.$ http://www.example.com/$1 [R=301,L]
I'm still uneasy about the sheer volume of 404's being reported in GWT, and 301's I don't even know exist not being reported, but as long as the user lands on the right page I can live with it.