If you copy out of MacDown's editor, the content is put onto the pasteboard as public.utf8-plain-text, eg:
Item 789514: public.utf8-plain-text: {length = 25, bytes = 0x23232320 48656164 65720a0a 54686973 ... 69732066 696e652e }
If you copy out of MacDown's preview, the content is put onto the pasteboard as rtf, html, et al:
Item 789514: com.apple.webarchive: {length = 1412, bytes = 0x62706c69 73743030 d101025f 100f5765 ... 00000000 0000054a }
Item 789514: public.rtf: {length = 496, bytes = 0x7b5c7274 66315c61 6e73695c 616e7369 ... 73206669 6e652e7d }
Item 789514: public.html: {length = 1146, bytes = 0x3c683320 69643d22 746f635f 30222073 ... 696e652e 3c2f703e }
Item 789514: public.utf8-plain-text: {length = 21, bytes = 0x4865616465720a0a546869732069732066696e652e}
Item 789514: com.apple.WebKit.custom-pasteboard-data: {length = 32, bytes = 0x01000000 07000000 0166696c 653a2f2f ... 00000000 00000000 }
Item 789514: public.utf16-external-plain-text: Promised
In both cases, MacDown should be placing content onto the pasteboard using the net.daringfireball.markdown UTI (encoded as UTF-8) as that is the official UTI for Markdown (cf: https://en.wikipedia.org/wiki/Markdown)