Depending upon how full your hive is, and the flow, there is a descent chance the bees will build some comb in the space. You could stuff a piece of 2” thick foam in there to eat up most of the extra space, or just risk it. This late in the year I would probably just risk it, and remove any comb if they build it.
Actually I have some 2.5” bodies on the tops of my hives too, but they have slats in them to maintain bee space.