This isn't difficult to understand. Hotels pay ~25% commission to online travel agencies. They really, really, really, do not want you to book through any of them, and they offer perqs for booking direct. One of those perqs is their loyalty program.
The agency wants you to book through their site so that they can earn that commission, and they offer an incentive (in this example) in the form of bonus points.
You can have one or the other, but officially not both. (
Practice doesn't always follow policy.) It does not bother me in the slightest that American Express gives me this choice. Sometimes I stay at Hilton or SPG/Marriott properties, but when I don't it's nice to have the option to earn some bonus Membership Rewards points rather than a few points in another hotel program where I will never accumulate enough for a meaningful award.