YMMV as to benefits.
Major room upgrades are usally not given except if demanded [ask not so nicely]. If your booking thru a 3rd party that's a reason for denial but abvisiosly it depends on front desk rep. They can see upon checking where the reservation was made.
In my past experience, I did get upgraded with 3rd party bookings but YMMV. My guess is, late check out and other benefits are usally easier to get with 3rd party bookings.