I really don't like debugging these older tkinter plugins. Even when they're my own!
What version of Sigil were you using (before the AppImage) where this was working the way you expect it to? I ask because I don't think this has anything to do with the AppImage. I can't get Ctrl+a to do anything in the tk widget in the Arch packaged version of Sigil 2.5.0 either. I can see the files that are highlighted in the tk widget (in both the AppImage and the regular build) and I can highlight the first file, hold shift and click the last file to highlight them all, but Ctrl+a does nothing for me--regardless of if I'm using the AppImage or not.
I DO notice that tkinter dialogs seem to be scaling differently for me from the AppImage to the regular build. Built then tkinter has always behaved squirrelly for me.