No, the gerber output should just reproduce the picture from the pcb viewer. If your description is correct (and nothing important missing), then this is a bug.
But I could not reproduce this behaviour with a quick simple test (used the latest v9.0.testing from yesterday).
try to install one of the latest testing versions and check if the behaviour remains. There were already many bugfixes submitted since v9.0.0 release,and some of these bugfixes affected also the gerber files.
attach the archived example (complete project, not only the board file) in this thread, so we can try to reproduce the issue with your specific project. If you want you may delete all unnecessary items from the board.
good pictures, good example. Looks really like a bug, provoked by the "“solder mask minimum web width” setting.
Would be good if you open a gitlab issue (Kicad board editor–>Help–>report bug report) and attach there your example and the pictures.
Does it make sense if the geometry is showed in PCB Editor and not in gerber files?
Normally not, gerber output and pcb display should be the same.
But there is a exception. All settings in the shown “Board setup–>Board tackup–> solder Mask&Paste” are only used for postprocessing the pcb prior to the gerber generation. So these settings (mask expansion, removal of mask < minimum web width) are not reflected in the pcb editor.