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The automatic identifiers are created by the reader, not the writer. In this case, the reader format is mediawiki, so mediawiki's scheme for identifiers is used (_ instead of -).
Actually, the extension gfm_auto_identifiers should be usable with mediawiki input (-f mediawiki+gfm_auto_identifiers), but it doesn't quite work because something in the mediawiki reader special-cases a - -> _ conversion. I think I can fix that.
Input file a.wiki:
Pandoc call:
pandoc --output=test.md -t gfm --toc --standalone a.wiki
produces
Online: https://gist.github.com/mineo/2b21f4d1e0ffa062adaef113037c2fb8. The test heading in the TOC links to https://gist.github.com/mineo/2b21f4d1e0ffa062adaef113037c2fb8#test_heading, but clicking on the heading in the document itself changes the anchor in the URL to https://gist.github.com/mineo/2b21f4d1e0ffa062adaef113037c2fb8#test-heading. These are not the same:
Github converts spaces in the heading to hyphens, pandoc converts them to underscores.
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