The default scope for markdowns in the atom is -.source.gfm, not text.html.markdown.
Your snippets will look like this:
'.source.gfm': 'Bash': 'prefix': '`B' 'body': '```Bash\n\n```' 'rubyonrails': 'prefix': '`r' 'body': '```rubyonrails\n\n($1)```'
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