Why is that a problem if you are already going to be using specific software to interface with your notes don't you want it stored in an optimized foolproof format that is also one the preferred format recommended by library of congress?
And if you want always direct edit access and do it often why not then a simple plain text since either way you will be dependent on the software if you like the additional features it offers which aren't inside .md like linking and other
And if you want always direct edit access and do it often why not then a simple plain text since either way you will be dependent on the software if you like the additional features it offers which aren't inside .md like linking and other