C-c C-a r should place reference links above file-local variables

[phst]

Create a new Markdown buffer with contents:

<!-- Local Variables: -->
<!-- mode: markdown -->
<!-- End: -->

(the specific contents of the local variable section aren't important)

Then go to the beginning (M-<) and use C-c C-a r to insert a reference link. Link text and URL don't matter. The link will be inserted below the local variables section; it should be inserted above.