Mostly depends on how you want to organize your workflow! I had been using a variation of Cat’s amazing workflow for a while but ended up hopping on the beta versions of Zotero, which don’t work with Zotfile and therefore don’t really work with Mdnotes.
Could you expand on what you mean by automating? For example, if you’re looking to incorporate highlights/notes from your Mdnotes files into a separate note, you can always embed/transclude the relevant blocks.