This line has me a bit worried: https://github.com/geany/geany/blob/bb45e3b7485e27f29bf652968b9094da322d0bc7... Project indentation preferences are stored separately, and appear to override editor preferences. The project preferences don't appear to have a checkbox for "tab key indents", currently. Should these even be Indentation preferences, as opposed to Editor Features?
Technically speaking, unindenting when using tabs may do something additional: with spaces, backspace unindenting moves the cursor to the first non-indent character (as does shift+tab, but not ctrl+u).