score:1
Most chains honor the perks if not the points on discounted/negotiated rates. I had to stay in Accor properties a few times on travel-agency booked rates, and point accrual wasn't allowed. But my Platinum card did get me the usual upgrade and perks.
Another thing to know with the points is that if two people travel together (on company business trips for instance), and one person is paying for both rooms, as can be the case if one has a corporate card, the points for both rooms might go to the person who pays. Happened to me a couple of times. Not a biggie, but it might be an indication that hotels separate the card perks from the points accrual based on the payment source.
Upvote:5
When in the same situations, I was given the perks but for IHG Properties where I have gold status. Basically at check-in, I asked if they had my member number with the reservation. They said no, so I gave it and they upgraded my room and gave me the usual Gold member perks.
It probably varies by program but usually check-in gives you the opportunity to have things changed.