At first sight this sounds like a good idea, but I'd be careful. Depending on what you put in the case, if the amp isn't protected, you could scratch or dent it and, if there is enough room for stuff to move about, maybe cause damage to the front or back panels, controls, switches and sockets. I'm thinking leads with 3 pin plugs, jack plugs and anything else with metal components.
I have always used a 4U for my 2U Thunderfunk. The extra airflow helps and I use the space to store the foam blocks I sit the rack on, to cushion the amp from vibration from the cab.