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How do users enter actual *text and **text in their content without enforcing the formatting?
(Not everyone will know about or will want to use the footnotes)

I've considered this before and we were worries about false positives, but maybe that worry is questionable. Input rules can be undone with cmd+z, Backspace, and Escape I believe.

Yes, the input rules can be undone via CMD+Z and Backspace.

That assumes the users knows about it.

I would just note that the convention of transforming text based on special characters already exists. If a user wants to start a paragraph with a hash # or a hypen - they have this same issue - the block is transformed into a heading or list and they have to learn to use backspace or cmd-z to reverse it. The same for using backticks inline (which can only be reversed with cmd-z, not backspace, I believe).

This would behave similar to the backtick character, in that if you have more than one in a paragraph, it will automatically transform the text in between, but you can undo it with cmd-z. Also it will not automatically transform any text that is copy/pasted or added out of order.