I’m pretty locked in to Calibre myself. I use a plugin called fanficfare to collect web fictions I like, which generates epubs and updates them when the stories get updated. Across those and regular books I’ve got about 6k books in my digital library. Right now it just runs on my desktop, but I’d like to move it to my server at some point.
As for actually reading them, I either plug in my kobo and manually sync/add books that way, or use the now discontinued Calibre Companion app on android to do the same on my phone. Unfortunately I haven’t found an app that is good enough to replace it for my needs, so I just deal with the app being unstable on the current version of android.

I’m similar, but it’s internal drives are planets, while external drives are moons.