Thanks all for the replies. Emailed the hotel directly for them to add the MR#, however they added the wrong number (Human error I guess). Rang Marriott and this time they were able to update the reservation and it now shows on my profile.
The Travel Agency owns my reservation, but at least I'm allowed to make a few small edits that don't affect the reservation itself. The 'local rate' was simply an offer between the TA and the hotel, so anyone qualifies as long as they book through the TA.
Also got told I will be eligible to earn points and on-property benefits.