One can configure ediff-filtered-filters such that it replaces multiple leading stars with one leading star and call ediff-buffers.
The following Elisp function my-org-ediff does that for you. Just copy the Elisp code to your init file, restart Emacs, and use my-org-ediff for diffing org files in the way you want it.
If you are content to use diff on the bash command line and are not looking for a pure emacs solution, you can use process substitution to pass into diff slightly modified files:
diff <(sed -E 's/^\*+/*/' file1.org) <(sed -E 's/^\*+/*/' file2.org)
Each sed command outputs its input file unchanged, except that a string of one or more asterisks at the ...