Unless through bolting, not just screwing, I would not personally use butyl for this application, and I sell the stuff.
If you have a wide enough portlight flange 1"+ a very thin bead of "shimmed" butyl, perhaps 1/4" wide on the inside edge, of 1/16" thick, works well as a spacer so you don't squish out all the other sealant out when drawing the bolts or screws down. It can also hold the port in place until the sealant cures, BUT, you need a wide interface flange which most applications do not have.
My general inclination is for mechanical spacers with proper thickness a jig to hold the ports in place while curing. If the ports are mechanically fastened, meaning through bolted, then you'd want at a minimum a "shimmed butyl" used for architectural glazing but I'd still opt for Dow 795, GE SG 4000 or Sikaflex 295 with the special primer.
There are good applications for butyl I just don't feel this is one of them just like a fuel fill flange is not. Butyl tape has very low adhesion so if you are relaying on it for bond then...well... I would not use it.. I don't consider screws into polycarbonate very strong as I have seen far to many strip out far to easily..