bookshelf looks like something you'd like. It doesn't seem to automatically index the files, but it does work without Calibre and has no UI. It only supports Epub though.
I don't know if it saves progress and I can't test it right now.
I'm not aware that progress saving is a default feature of OPDS. There is some work being done in that direction, but I don't know of any server/app combinations that do that for ebooks.
Apart from that, I'm relatively happy with kavita. It comes with a web UI though.