Doing it like the help overlay would be much better for me. Since much of my course revolves around glossary usage having it come up with the header/footer and bread crumbs would be nice.
Voted for the issue. Since I'm systems guy and not a programer I've had difficulty in finding where to change it. I had thought I could use the files from an older moodle version to make the change. Nope.
I've contacted theme devs to see what it would cost to do it. According to them the glossary popup can not be handled by a theme change.