This behavior is designed that way by Mozilla. There is a note about that, which explains that an extension has to proactively delete these entries by modifying the browser history. If I'd do that then I can almost hear people asking why Tampermonkey needs to access all their past browsing activity. :(

Maybe I'll implement that by using an optional permission, but that is some effort to implement...

https://developer.mozilla.org/en-US/Add-ons/WebExtensions/user_interface/Extension_pages#Extension_pages_and_history