If a project is renamed or relocated from one name to another it might (and should) preserve issue and merge related information and discussion, but any full URLs will have changed, making full URLs fail in specific cases. Using any form of shortened sequential identifiers will fail when referenced in commits merged in from forks of the project that have their own conflicting identifiers.
To solve this in any real way there needs to be a way that when a project is forked it carries information about issues and merges with it, and when commits from that fork are merged back into the main project, or merges from a fork of a fork are merged all the way back to the original project, all metadata about those merges are carried to the original project.
Linus' argument is that the correct place to store that is in the merge commit's message. That it is the responsibility of the person doing the merge to provide that information, and that GitHub does a bad job of providing tools to do that.