It's not something I would normally consider in a layout for a toilet. Like you mentioned above, it's common to roll for a vent to be above the flowline of the pipe, but not done much for waste.
If given either option, would it be better for a 3" closet waste wye coming into the main 4" waste line to be flat or rotated up some amount? I know that vents must be rotated up, but waste wyes? It seems like waste flow would be better if it was rotated up, but then again, perhaps the water would wash out too quickly. I'm curious if you have an opinion.