So the assertion is that Matematica should only be expected to work with Metacity or KWM? Or is it that Mathematica depends on a specific desktop environment? Either way, that is a bug in Mathematica...
EVERYTHING in Linux is, more or less, "unfinished." That emphatically includes Gnome and KDE, as well as window managers. That is why we have standards. What, specifically does Mathematica depend on that exists in both Gnome and KDE and not in openbox, i3wm, etc? That is, why do you need a desktop environment? If Mathematica for Linux depends on a specific desktop environment, or even a specific wm, that is a bug.
"Unix software" which doesn't work with Unix shouldn't be sold as such.