I often book through conference websites and through my company's travel team and I've never failed to get points/stays and the appropriate benefits for my status at the time. Booking through the Marriott website offers a few benefits for non-elite program members, but if you are already Gold or above I don't believe there's any benefit to booking through the Marriott site.

If you book through another route and get deeply discounted rates then those may not give you points/stays credit, though.