chewitt ,
the logic for manual installs from zip is not annoying and works fine, looks as intended. I have actively tested this with LE13 nightly.
Also if the add-on has been installed from zip, an available update from LibreELEC add-ons repo will be announced. At this point you can decide to accept or ignore the update. It will not automatically updated via "Install auto updates only" or a background schedule, because the current installed version is not from a repo, thats the only different I found.
If you accept the announced add-on update from repo via "Install all updates", then you will on track with the repo afterwards and will get all future updates from the repo.
In addition, it is possible to switch to the zip version with the same add-on ID from GitHub, if required. This can be helpful for those affected, for example, if a new version with an urgent change is available but the build/publishing process for the repo has not yet been completed. As soon as the add-on version becomes available in the repo, you can switch back to the repo version and it will be updated automatically from then on.
Of course, it's easiest to just use the repo version. That was the main reason for including it in the repo.