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I know this is going to stay on the back burner for a while, but I hope we can keep it in mind -- so I thought I'd put in this issue.
I think subsetting to a polygon is a really import use-case -- there are times, where a rectangular subset might be massively larger and more complex than what is needed -- it can also create disconnected domains -- which I'm not sure are a real problem, but still ugly.
It's possible that keeping polygons in mind might lead to different design decisions -- it's also possible that it wouldn't be a huge lift: you could subset to the bounding box of the polygon first, and then subset tot he polygon with a less efficient algorithm -- maybe that would be good enough for a first pass.