The main thing is, would it be getting more air there than next to the other one where they'd be pretty much touching?
Well, with the GPUs touching, the top GPU wouldn't get as much airflow (which I was hoping to fix through the heat sink on the MSI). The other way, the PSU would be venting hot air into the GPU through its own fan (assuming it's an exhaust fan) or it could be competing for air (assuming it's an intake fan) with the GPU. If it's venting the air upwards, the heat sink might help with that as well?
My motherboard isn't great for this, but with the new Intel socket on the horizons I'd be hard pressed to upgrade that now.