I am a meeting planner, and this is roughly how it works:
* You bring a conference to a city and as the meeting planner you negotiate directly with each hotel on rates and such. The only exception is there is a single sales department that manages several hotels. e.g. Currently in Long Beach, I dealt with one sales rep for both the Renaissance and the Courtyard. However, the whole point of this is these are rates that are provided directly by the hotels for the specific conference.

* Then instead of using the hotel's primary reservation system (marriott.com), you might use a 3rd party solution to manage the sales of all of these rooms and possibly present them together to attendees. e.g. onPeak, Passkey, etc. These third party systems just make it easier for planners and attendees to manage/navigate the blocks. They (the 3rd party solutions) aren't necessarily getting a commission and they are only still selling the rooms that the hotel contracted with me (as the meeting planner) at those rates. And the 3rd party is something you select during contracting, but the hotel really doesn't care. They would sell it all via 1-800-Marriott if you wanted them too.

This is a really basic description, but the point is that these are still Marriott reservations based on the directly contracted rate. These aren't discounted rooms that hotels.com is reselling. And trust me, while the rate looks cheaper than rack, when you are dealing with the larger blocks of rooms, the longer lengths of stay, the use of meeting space and F&B spend, and all the incidentals, the hotels are making out just fine. They are not considering this a discounted room in any sense. So yeah, you will always earn points as long as you are paying and it isn't going to a master. (In fact, as a planner, I almost always have my personal room billed as Individual Pays Own, instead of having my room go to master, so I can earn my own points on my stay.)

I would ask that you don't bother a Sales Department with this question. They will tell you that you will earn points. (If you want to ask Reservations, sure, but I think you should leave Sales to do Sales. Think how most companies separate Sales from Technical Support.)