There're a few Markdown variations or 'flavours' out there that implement footnotes (besides Php Markdown Extra, which you mentioned). Those I'm aware of are Pandoc's Markdown, R Markdown, ScholarlyMarkdown, and MultiMarkdown.
I believe footnotes work this way in all of these variations:
This is some text with a footnote.[^] And another.[^]
[^]: Here is the first footnote.
[^]: Here is the second footnote.
Or inline:
This is some text with a footnote.^[Here is the first footnote.] And another ^[Here is the second footnote.]
They should both render this way:
This is some text with a footnote.1 And another.2
- Here is the first footnote. ↩
- Here is the second footnote. ↩
You can add links to footnotes too, for instance:
This is some text with a footnote and link.[^Here is an example of a footnote with a link at the end. [link](http://stackoverflow.com)]
Which should render like this:
This is some text with a footnote.1
- Here is an example of a footnote with a link at the end. link ↩
Btw, if you use an editor such as Atom or VSCode, you may want to add the extension Markdown Preview Enhanced. As the name indicates, it allows previewing the rendered text as you type (it supports previewing and exporting with Pandoc).
Pandoc's documentation on the matter: https://pandoc.org/MANUAL.html#footnotes