Plenty of episodes where crew members get trapped in caverns where the transporter can’t reach and they have to set up pattern enhancers. I would assume the miners are done ng just that, setting up pattern enhancers to increase range to whatever they’re trying to get to.
It also makes sense that ships would have overpowered, top of the line transporters and replicators. At least the best ships. I would assume that there are different spec l, lower quality devices in use. This was my main takeaway from lower decks. We’re used to seeing the best of the best on the enterprise. So yeah, if all of Starfleet was that good, both tech and people, they wouldn’t have so many problems. But it evidently isn’t.
I hope someone gives you a good answer, because I’d like one myself. My method has just been to do this stuff little by little. I would also recommend calibre web for interfacing instead of calibre. You can run both in docker, and access calibre on your server from whatever computer you happen to be on. I find centralizing collections makes the task of managing them at least more mentally manageable.
You might want to give an idea of the size of your library. What some people consider large, others might consider nothing much. If it is exceedingly large you’re better off asking someplace with more data hoarders instead of a general Linux board.