Hey,
I didn't really follow the thread in depth, so sorry in advance if I missed something obvious.
If it does indeed come down to just hiding widgets, I think we could offer a way to do that. We (or Mint guys) could have a 2nd Glade file which has the visibility of much stuff set to false. Other way is to maintain an array of items to hide on startup. Both of these ideas were shared here I think. I made a quick and dirty patch to show the later form:
If it is even only about hiding widgets which already can be hidden via menu items/config options (via config even more can be hidden than via the GUI, e.g. each single tab in the messages window at the bottom), then it might be even enough to provide a global geany.conf in $prefix/share/geany, see http://www.geany.org/manual/#global-configuration-file
Regards, Enrico