No, Alex - this is too easy to test, scientifically.

Just FTP a cruft-file up to a plugin or theme that is about to be updated. Follow through with the update. Observe the cruft-file vanish.

Just now I had 2 plugins that were ready to update. (I get the notices, but I have a plugin that lets me do it with my own fingers.) I created a text file called "test.txt", containing only the word "test", and saved it on my desktop.

In FileZilla, I navigated in my remote shared hosting environment (I also keep localhost environments) to the plugin that I am about to update, and uploaded "test.txt" into it. Then I hit Update in Admin. Then I hit Refresh in FileZilla. "test.txt" vanishes, right before my eyes, and all the file-dates change to today.

Orphan files etc do not hang around in wp-content subdirectories, when a theme or plugin is updated. Those of us who tinker around with our own files in these content-subdirs, have known all along you have to have the mod-files somewhere else, when you click the update-button - or they're gone.

Maybe you're thinking 'Linux', Alex. Ubuntu does quite a bit of 'leaving' of files for apps & packages, when they are updated or removed. We have a special app for hunting these down ... and in an active environment we may have a series of the same file, with different dates or identifiers ... and can revert or reset to a previous state, etc. Config files (of which Linux is fond) may also retain 'dead' values & settings.)

Not in anything like a modern WordPress, though (and probably not in PaleoPress, either).