My answer is to use a window manager like wmaker or blackbox. Seeminly, they handle the EMBOSS windows perfectly and Exposé treats them like normal windows. Phew.
Problem: when using non-Apple window managers in rootless mode, new windows (like xterms etc) tend to open underneath the Aqua menu bar at the top of the screen. This is a pain, as you can't reach the Close button. However, if you use wmaker, you can fix this as follows. Find the configuration file (~/GNUstep -> Defaults -> Windowmaker) and edit the lines to read as follows:
WorkspaceBorderSize = 22;
and
WorkspaceBorder = TopBottom;
This will stop windows being opened under the Aqua menu bar, and you get the added bonus of being able to use the WMaker dock - which is just like the Aqua one, but can be set up to launch S11 apps.
Notes:
- This will apply to the Jaguar x11 also.
- The setting of 22 for the workspace border is higher than the maximum value available using the in-built WPrefs (WMaker preference setting program), so you should re-do these changes after you have set all the other settings with WPrefs...
- Install all the above using Fink

