@EastEriq @nhedgehog: thanks for your help!
Just try to run the last nightly with ./luajit -joff as stated above and without any other change.
You don't need to run gdb or any other tool, just keep a look at logs and report segmentation faults (please remove old crash.log to avoid confusion

)
Since this is painfully slow (specially for screen transformations like inversion or rotation) I would suggest to enable C blitter unless that makes the program crash (In developer options, see attachments)
Just try to read books and explore the UI/Menus. As @nhedgehog said the behaviour isn't affected by big or complex files. It just happens randomly when the GC hits in.
Also, if you don't mind, please lets move conversation to
https://github.com/koreader/koreader/issues/6000 because it is easier to paste diffs there and keep track of reports. If that's not possible it is cool for me to stay here. Moderators can move this thread to dev's corner if they want