From experience I am almost certain the issue has to do with architecture, the original developers didn't properly consider UX when making the first steps and that has shaped how everything else was implemented in it, and this is the end result. Fixing it at that stage is way too much work as you said, rewriting all tools and the UI from scratch would probably be the easiest way to fix the UX at this point. If it was easy then it would have been fixed as it is an open project as you said.