If I understand your questions correctlly this is my answer. You cut the port material to the length needed IE: 3 1/2". The actual port cut out is just a hair bigger than the 2 1/2 diameter. I cut a 2 1/2 hole and then when I got the port material I used my dremel with a sander tip and opened it up just enough to get the port in. I then coated the end edge of the port with some PL (I used PL on all my 2pi and 1pi cabs) and slid it in even with the baffles front.
So long story short cut the port to 3 1/2" and slid it in all the way through the front/baffle until it reaches the outside edge.