Certain EXIF tags, for example many of the QuickTime tags listed here, are non-writable by common EXIF editors.
This list of writable vs. non-writable is maintained by Phil Harvey's exiftool, but I have found similar results attempting to edit the same tags with other tools such as MetaClean. My edits to these tags do not persist and the original values return when I reload the file.
Why is that? What about a certain tag makes it uneditable, and is there any manual way to override this?
First, the tags you linked are not EXIF tags, they are Quicktime tags. EXIF is just a common, but narrow subset of all types Metadata. Sorry for being a pedantic ass about it.
In the case of exiftool and especially video files, the standards and formats for such tags is, as Phil Harvey (exiftool author) has put it, a complete mess. There are apparently a lot of differences in how various programs and cameras implement such metadata. Phil doesn't feel he has time to troubleshoot all the various differences and edge cases. To give an example, he recently started adding read support for gps tracks in video files. This ended up ballooning to having to support over 20 different variations of geotracks. And that's just for reading.
Followup: As of exiftool ver 11.39, a number of the more useful tags have been made writable. Exiftool now lists them under the group ItemList instead of Quicktime, though they are still part of the Quicktime group.