I do no longer get a crash, but at least at certain points
during the generation, minimization is possible.
Even the help balloons for the menus keep working.
When playing around with this, I actually managed to get
the main window minimized and visible but non minimizable
at the same time...

Please test what happens when you minimize the window,
while waiting. When doing this using the generation of
the user manual, I obtain the message:

QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::end: Painter not active, aborted

As to the version issue with Qt: yes, this is frustrating;
with Guile, problems have been at least as bad and frustrating.
When the problem is severe, then we should #ifdef suitable hacks.
If the problem is not severe, then we may just leave it.
At any rate, we should keep a systematic record of problematic
issues for various versions of Qt. Could you start such a record,
and think of an appropriate place where to put it?

There are a few problems with the new wait widget:
  1) It is centered on screen, not inside the window.
  2) You could add a small indication 'TeXmacs busy'.
  3) Dark red on yellow was a bit nicer, in my opinion.
  4) The wait widget does not disappear after completion.
  5) The state of a previous wait widget is not restored,
     when finishing a subtask.
You may try 'Help -> Full manuals -> User manual'
in order to experience the problems that I notices above.

Implementation of wait widget in Qt port of TeXmacs.