I do not think that Monarch scheduled flights are covered by ATOL. An ATOL certificate must be issued at the time of booking and certainly this has not happened on my next three bookings. From memory ATOL certificates have not been issued for over a year.
Bookings with Avro are covered by ATOL. Bookings for flight plus accommodation are covered by ATOL. Packages are covered by ATOL.
Monarch scheduled flights booked on their website are Atol protected, and they issue an Atol certificate. I've just flown Monarch and one of the flights was only booked a few weeks prior, and yes I got Atol certificates for all of them.
Monarch bookings done via Avro used to be for charter flights, but Monarch no longer operate any charter flights. Now Avro is just an advertising platform for shonky OTAs to advertise on.