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