PDFs getting defaced when opening through "Preview" on MacBook with macOS Sonoma

To find out if it's system wide or user specific, try this...

Open System Preferences>Users & Groups, unlock the lock, click on the little plus icon, make a new admin account, log out & into the new account.

Does it work in the new account?

Please do the test on a new user as BDAqua requested.

And then let us know; also: Please run Etrecheck and post its full report here. Use the "additional text" button and paste the report into the text box.

Preview does not handle all PDFs, and to that degree, it depends on what software generated the PDF and what content Preview parses, and the content it ignores. Adobe, on the other hand, has the ability to keep Acrobat Reader current and capable of handling content that Preview does not, since they do not charge themselves any exorbitant royalty to update their own PDF library and application.

For the test, I saved the Word file to PDF, opened it in preview and saved it under a new name, it was cleaned...

Saved the Word file to PDF in what application?