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I hadn't looked before so I did a little investigating. With Calibre 4.23 on Linux, I found that it's not exactly Calibre, it's the Reader.
I don't know why this Reader (it's a newly re-written reader, but I don't know if the old one did this) is modifying the epub meta-data. There is no reason to do so that I'm aware of as bookmarks and other reading information is kept in the database.
With that in mind, I changed the EPUB file permission to remove write permission. As a Read-Only file, everything seems to continue working normally and the Reader is no longer capable of changing it.
So at this point I can only suggest:

Change all the epubs to read-only
Substitute a different reader
Send feedback to Calibre

additional info
I did a little more investigation and found that "ebook-viewer" is writing meta-data under "Miscellaneous" "calibre_bookmarks.txt" even though bookmarks are controlled via the database. Deleting this entire entry via "edit book" has no effect and the book marks are still present because they are in the DB.
The content written also includes: access time stamps, Book Title, and my User ID. It's written as JSON Base64.
This should not be happening!
I posted Bug #1894442
Calibre Response
Calibre says it's not a bug because most users prefer it this way. Nevertheless, it can be turned off by:

LTrun {sic} it off under the miscellaneous section of the viewer
preferences.

Open the Calibre viewer
Right-click the body of the book to bring up the controls
Select Preferences
Select Miscellaneous
Uncheck "Keep a copy of annotations/bookmarks in the e-book file, for easy sharing"

I verified that it worked (at least for one in a row).


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