Two advanced settings are needed to make BBEdit treat all new documents as Markdown format, and to save with the correct file extension. They are:

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defaults write com.barebones.bbedit PreferredFilenameExtension_Markdown -string "markdown"
defaults write com.barebones.bbedit DefaultLanguageNameForNewDocuments Markdown

If you use TextWrangler, replace the “bbedit” in the above with “textwrangler”. But I’d recommend purchasing BBEdit instead.