I have booked third party reservations a few times when it was a better deal, and have received minor complimentary upgrades a few times, things like standard view to garden view. I was not treated any differently than someone with a reservation booked directly with Disney. Upgrades are done at Disney’s discretion for their operational needs. The best advice is to book the room you want when you make the reservation rather than relying on an upgrade.
If you want to know if an upgrade is available, you will need to go to the front desk for check in and ask what it would cost to upgrade to the room type you hope to stay in. If it’s in Disney’s best interest you might get lucky and get a complimentary upgrade, or you might have to pay to upgrade, or there might not be any availability to upgrade. I would give the same advice regardless of whether the room was booked through a third party or not.