The minimum width of the panel which shows you controls of the tool you're currently using in the "Edit panorama" window is far too wide. Example with the "Move" tool: http://i.imgur.com/d0fBLGs.jpg Furthermore, not only is it far too wide but the arrangement of the contents of this panel is not fluid. There is no need for that huge gap between the labels on the left and the icons on the right. APG-4.* in Linux.
Great that it's on your radar. I've always had it regardless of window manager - KDE4, KDE5, Awesome, and possibly E17. Maybe it will help you reproduce the problem by knowing that I always use the "LINUX .TAR.GZ 64" version and run the ./AutopanoGiga.sh file.
Indeed, I even think it's not linux specific (we had similar issue on macos and windows). What is the display resolution you're using? (I think its related to small screens but not sure though).