alt Hacker NewsA few months ago there was another of these posted, called Epiq: https://news.ycombinator.com/item?id=48155570
My comment on there is about a surge in popularity of these over a decade ago, with a link to a previous comment about problems I remember them having that prevented them from being usable for most people ( https://news.ycombinator.com/item?id=47956979 ), because of their intended design rather than an implementation issue. For example bullet 3 was a problem in one, that another tried to solve with bullet 2.
I don't have time right now to look at this one to guess if these apply, but might be interesting/useful for someone else.
Other than the first bullet point in your list[1], my contribution in this regard addresses everything else.
Don't have a link handy but it's on github called "rotsit" (revenge of the something issue Tracker).
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[1] That's the entire point of having the issue tied to a branch: if an issue is marked resolved in the branch you are looking at, then its resolved in the branch you are looking at. Storing the issues independent of branch means you need to also store extra metadat about which branch it is broken on.