The definitions of an application fee and an origination fee in my mind are different, but your definition can certainly vary. Regardless, the MAPR rules address this based on the plain language of the term, "application fee" and it's included:
https://www.bankersonline.com/regulations/32-232-004232.4(c)(1)(iii)(B) Any application fee charged to a covered borrower who applies for consumer credit, other than an application fee charged by a Federal credit union or an insured depository institution when making a short-term, small amount loan, provided that the application fee is charged to the covered borrower not more than once in any rolling 12-month period; and