Thanks Rich. My prior method of overriding the FLWM binary, dropping out of the WM, and running startx (with a unique WM name in /etc/sysconfig/desktop) was not playing nice with the default desktop init stuff, so I changed things up to boot FLWM (from the .tcz) normally, then after I drop out of the WM, instead of just running startx, I have a wrapper script that can make a backup copy of the FLWM binary in /usr/local/bin, then replace the binary with my experimental FLWM build, then issue startx. Now I have all three sub-menus on my FLWM popup menu.
I'm also happy to report I've solved the weird "windowshade" rollup window minimize feature for the non-FLTK windows. Not sure it was really because some windows are not FLTK-native, but in any case, I have every type of window minimizing and coming back to normal as expected. Screenshot of the topside version with a few minimized windows (just showing horizontal titlebar strips).