Could happen the other way around too.... room allocation depends a lot on the front desk when they block or check in rooms. When you buy a room from one of the OTA sites, look somewhere in the fine print, it should say that bed and room types are not guaranteed. They buy ROH, run of the house rooms... so you could end up anywhere. But a good front desk manager or agent that blocks rooms, will give the best rooms to "their" guests, then will look at the rates you paid and assign accordingly and others just hand them out as you arrive and what's available at the moment.
When you can book with the hotel directly, you should. Because then YOU are their customer, otherwise, Agoda or Booking.com is their customer and you are Agoda or Bookings customer. Most chain hotels will only give you your "status" benefits when booked directly with them, you might find a manager or a hotel that will honor your benefits, but they're not obligated to.
Hotels in Asia are weird, they seem to prefer that people book online and put their own rates too high, I don't get that strategy.... not when so many use the internet. Chris at The Venue, will usually give the same or better rate than what the online sites are giving as does Classroom Suites when you book directly with them and some food credits, that logic I understand because they get their money right away from you and pay no commission.