I found that following the notes presented in /usr/share/doc/arduino/README.Debian for non-reparenting window manager users (i.e. “export _JAVA_AWT_WM_NONREPARENTING=true”) make the behavior I mentioned disappear.
I would just ask, then, to make it a bit cleearer in the README: it mentions that non-reparenting window manages “will only display empty gray windows”; it does not match my experience (I got a non-resizing small text window instead of using the full available space). But I think that just adding this note would be enough to considering this bug dealt with. Thank you! — Gunnar.

