This is a larger task than it might seem at first. Each markdown card is rendered with it’s own markdown-it instance and has no references to the overall mobiledoc/Koenig renderer or other markdown cards so there’s no way to co-ordinate footnotes across cards. There would need be some form of architecture put in place for handling footnotes within a mobiledoc renderer instance that can be hooked into from disparate renderers used within cards.
TL;DR; don’t expect support any time soon, sorry.