Yes, as H said. The 100-400 AF is no slouch, definitely not a nuisance. But I whacked Dennis' 400L on my camera during one of our macro get-togethers, and the AF was noticeably faster. That's all I'm saying. More than likely it will not be an issue. I reckon it would be for things like birds in flight and the tracking focus modes.
I didn't mean to bring it up to turn you off the 100-400. It's a great lens. Just wanted to add some hands-on experience and alternate thoughts to your research
As I said above, you will be equally happy I'm sure with either purchase. In your case, I'd be inclined to go with the 100-400 I reckon.