[Ken Maltby]

You can avoid the processing of your library of ebooks/documents by not using the stock readers and placing the library behind a hidden folder. Koreader and CoolReader can both be set to read such "hidden" files and folders.

The File Manager in Koreader is simple but does include Cut, Copy, Paste, and Delete - as well as, a "Sort order" and "Reverse sorting" options. There is now also a search "Find a file" function for the File Manager. Also, you can search "Find a book in calibre catalog" function of the catalog calibre places and maintains on your reader, if you send books to your device using calibre. So Koreader's File Manager is not without its interesting capabilities.

With the Wifi on you can access OPDS catalogs and download books off a number of sites on the net, as well as local ones like calibre's builtin server. There is also a "Calibre wireless connection" that used to be called a caliber companion plugin (but that name is in commercial use), with that you can send books from your PC calibre library to your device. Other WiFi functions in Koreader include ZSync, and Evernote plugins, and a new "Progress sync" between Koreader devices. These uses of the WiFi do not contact Kobo.

The alternative readers are not slave to a database like the stock readers and user interface are, so there is no lengthy "processing" of the "hidden" books, that you can read with them. No "Sync" required either.

If you use The Kobo Start Menu (KSM7) or Advboot to launch Koreader you need not start the stock software at all, avoiding the issues you mention.

Luck;
Ken