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I know this may seem like a silly and tiny issue, but I can’t understand why they do this (take for example tic-git (https://github.com/schacon/ticgit) which appears to be quite popular). Surely it would be better to place the data in a folder and have it in every branch, so modifications to the bug database can persist across branches and merges, and bug fixes can be tied to the commit which resolved them?
Yes, that’s the other approach, which Bugs Everywhere uses. There’s an old LWN article that does a survey of Distributed Bug Trackers as of a few years ago that may be of interest.