Footnotes plugin is compatible with AMPforWP. It does not require any 3rd party addons to work with AMPforWP.

What features are compatible at the moment?

1. Allows Superscript layout.
2. Allows Mouse Over Box.
3. Support the Hyperlink Symbol in the Reference Container.
4. Gets connected with Collapse references by default option.

If your required Footnotes feature is not available, then you can request it from this support page.