You don't have to allow Kobo to process all your ebook library, you can hide the files from the Kobo processing. They can be read with one of the alternative reading programs like Koreader or Coolreader. See this
install guide. It includes info on how to create the hidden folders.
I have an ~7000 file library with ebooks, PDFs and documents of many kinds in the hidden library and read them mostly with Koreader. I only have a few that I let Kobo see.
Luck;
Ken
P.S.; Koreader is in another period of rapid development with several unique features recently added, including OPDS support, a calibre companion plugin, suspend display of book cover or not, and several others. (Not all of these are in the official release download, but most are on the Over The Air (OTA) server). (The OTA is for wireless updating of Koreader, I prefer to just download it on my PC and copy/merge the koreader folder, to do the update.)