The .cson file is a json file that includes a bit of tagging specific to Boostnote. I agree, it’s not ideal to have to keep modifying them, but you shouldn’t have to export them to Markdown until you’re ready to use them elsewhere.

I imagine that a command line based exporter could be modified to automate exporting files, but you can also rename the files to .md and use them as-is, albeit with the Boostnote tags attached.