I removed the flatpak, redeployed the most recent version and tried to start zettlr with the parameters.
--disable-gpu : worked, zettlr 4.0.0 started and fully opened
--ozone-platform-hint=x11 : did not work
ps.: as I am on KDE, i searched for Zettlr in the startmenu, right clicked the icon, choose "edit application" and added "--disable-gpu" at the end of the command-line arguments, clicked save.
now it automatically starts with --disable-gpu and I dont have to start it manually with console. it automatically worked with my shortcut which was pinned to the taskbar.