Since you're highly concerned about privacy, turn off your Wi-Fi and keep it turned off. After that, perform a factory reset then bypass the registration using SQLite3. (To the person who called concern about privacy paranoid, some people have much higher expectations for privacy. In many cases, there's nothing paranoid about that. It is simply how they choose to live their lives.)

Avoiding the database rebuild or database corruption pretty much means avoiding Kobo's reader software. The great news is that a few developers have created alternative reading software for Kobo, and that it has features that go above and beyond what Kobo's software provides. KSM + KOReader is my preferred choice, but you also have PBChess from vlasovsoft.

On the File Manager in KOReader, I was in error earlier. It has rudimentary file management functionality. You can delete files and move them. As far as I can tell, you cannot create directories or rename files. I just reinstalled PBChess. It has a more comprehensive file manager. PBChess also includes a few useful utilities and games, some of which are free and some of which are shareware.

There are plenty of options available for your Kobo even if you don't like how Kobo does things themselves. They also work well alongside each other, in case you want to pick and choose or experiment to see which you like best.