If you pay for the room (even if you are reimbursed by someone else such as your employer), you will generally receive points. The outliers are industry rates such as for TA's and the like or other codes which expressly exclude benefits.

The difference here is that the room is directly billed to a master bill and paid by the conference organizer.

As to OP's underlying question about the rate, it is relatively meaningless as the conference likely has many other services such as conference space, food & beverage. All of this is fungible. For whatever reason, the room rate may be high and a conference room may be included or, alternatively, the conference organizer's room may be "free" (but actually split among the attendees'). In the end, all that matters to the property and the organizer is the total. But, the individual event planner may care that his bar tab is comped !