Ohkay nvm. I stumbled upon an answer on LS1Tech. Here it is in case anyone else has the same concern:
ScottyBG*, 12-17-2016 09:19 AM
"If you look at the head, the pointy area at the top of the port lines up with the injector. Originally the LS cathedral head got the cathedral shape to allow the fuel injection to shoot fuel into the inflowing air stream more efficiently. Old school it was all designed around carburation, and airflow (air with evaporated fuel in it) as the only consideration. If you consider the head, without the "gable peak" on the port for the injector to shoot fuel in, the rectangular area of the head and the intake match quite well. So the addition of fuel injection, as a new technology, changed the way of thinking regarding matching head and intake ports. On a BBC the cross sectional area of a rectangular port is considerably different, than an oval port, and flow very different. The ports in your LS6 manifold flow appropriate amounts of air for the ports in your LS6 head.
You still don't want to try and put an LS3 or LS7 intake on a cathedral port head, that truly is a mismatch, because the volume of the ports are so different..."
I honestly did not know this.
