I've had one or two check ins where I got there late at night and nobody was around. When I said my name they checked the room I was in and then scooted me over to the "private check in" to do exactly what they could of done at the first desk I was at.

I would definitely say it makes a difference. It shouldn't but it does. As others say the staff would know the layout of the hotel and would know that you are in a more expensive room. Possibly they might think there is a better chance of tips from someone who has paid $1000 a night rather than $200.