There shouldn't have been a dependency error with wrye bash it has all in one installer. I've not seen path problems, for the larger mod I let wrye bash unpackage/extract the mod before installing.
If you count Ubuntu and all disto's base on it as one, then it would top the list.
Cutting Edge, Minimal testing, and Ubuntu has a history of bricking systems. The LTS is a lot safer.
That error is from a dependence missing from your system, the flatpak'ed Kega has been compiled to use the flatpak runtime (a separate runtime from the system), this will have all the dependences required by kegaFusion.
The flatpak is container holding all the dependencies the program needs
With Lutris you can script the install process.
Firejail is another option
An epub is just an archive containing text files, css files, and images, there nothing in there that can damage hardware. It's possible you just ran into a bad batch of kobo's