(developer here)

Interesting to hear that you think this is the opposite of how Obsidian works. I specifically opted for this approach so that these note codes are entirely independent of Obsidian itself and can be ported over to other solutions.

The other way to do it would be to store note codes in some vault-specific storage, but then those codes would be tied to Obsidian, which worries me a bit.

That said, I do want to figure out a nice way to improve it. One idea I've had was to introduce a cache of sorts, so that the plugin will remember all the older codes a note previously had. Do you think this would help your use case?