The code below:
some deep thought who needs a reference[^1]
[^1]: Here's the reference.
Should look like a subscript (and it does that way in the post preview), but after posting instead renders as:
some deep thought who needs a reference[1]
Here’s the reference. ↩︎
We have display footnotes inline enabled on Meta, so they do look like that here. Have you tried it on another site with that option disabled?
Indeed, it works. Thank you. I must have read the plugin topic inattentively
It’s pretty counterintuitive that the preview looks way different than the final post though.
This is true. I’ll slide it over to ux for consideration. 
Update: It was also mentioned in this topic too - Add numbering formats to Footnotes