Caps are generally low enough to go underneath the card when installed, and from the pictures it looks like your board is no exception. With some board layouts you may obstruct other features (sata ports are the most common one), but I've yet to see one that blocked a slot completely.
So I'll have to refer you back to my original post. The board should not obstruct the card, but your case size and design may limit its size, as well the output of your power supply. We'll also need to know a price range you're looking at.