Hotels play all sorts of games with this, including throwing in free stuff if you book direct ("it's the same rate") and doing "non-advertised" rates through loyalty and reward programs.
If you can't book directly with the hotel, it's very likely they don't have technology sophisticated enough to do a direct booking. You'd be surprised how bad hotel tech is. And the thing is, none of the independents want to spend anything to improve the situation. It's honestly madness.