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.

Is use wrye bash and loot (windows version)

With Lutris you can script the install process.

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