This person is correct. For stays booked through third parties (Expedia, Priceline, etc) they are technically not eligible to earn night credit, points, or elite benefits. Most of the time, however, hotel associates will provide some benefits or recognition if you tell them or show them your card.

Your best bet is to get the hotel staff and especially the reception or front desk associates involved. They are the ones responsible for submitting points to Marriott Rewards for credit and also for arranging benefits.

Customer Service representatives are usually bound by what the official policy says. Because they're being monitored and scored, they sometimes can't "say it like it is" even when it's asked directly. Hotel associates can be more candid and easy-going because they are (usually) not being recorded.