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I'm aware of this issue. The simple answer: the way Atom allows to parse content doesn't allow the detection of new lines in a pattern, which is needed to detect setext-style headers. See the FAQ on this. Unless the way grammars work are fundamentally changed, setext headers simply can't be implemented.
My headers using atx-style appear blue.
But when using settext-style (https://daringfireball.net/projects/markdown/syntax#header) they are not.
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