Alright, I got some time to set up another virtual file in IsBoxer. It works fine (especially with the "exit Glyph when launching" setting), but the "remember login" setting in Glyph doesn't work. Glyph checks with the server what the last login was from a computer and it won't match, so it will always show the Login window anyway.

I also had an issue with updating IsBoxer on one of my machines so it took a little while to get it updated. When I finally got it updated the virtual file feature didn't work on that computer because it lost the "multiple computer" setting and didn't get the new broadcasted IS settings.

Anyway, with GlyphClient.cfg added as virtual file everything now works pretty much exactly like it did before Glyph got released. The only difference is that the launcher window has a new Window Class name and the Login and Play button is at a new location (this may not matter to anyone else but me).