I used the SE gaskets when I installed the V&H power duals. Not a problem. Just a note, the original gaskets were compressed past the seating surface into the exhaust flow path.
The SE gaskets are difficult to maintain position and get a good seal with if you're not extremely careful (and maybe lucky). The stock gaskets crush, and might impede on the exhaust port as you said. I normally install the exhaust with the stock gasket and let it crush, then remove it and trim the part impeding on the exhaust port, then reinstall the headpipe. A lil extra effort, but you wind up with a good performance gasket, AND with a good seal that way too.
Hoist!