In a stock enclosure there is no way two round ports would fit. The flared ports also take up a lot of area on the baffle.
I am in the middle of my 4 Pi build. I modified the enclsoure size to increase the bass response. Right now, I have them taken apart to do the veneer and trim work. I will do a build report in 2-3 weeks after they are done and I have had time to do some sound measurements. I tested them before finished to make sure that my modified design did not have major sound issues that would cause me to have to cut the enclures apart again. They sound really good and I had a hard time putting my old speakers back in place.
The larger cabinet size dictated larger ports or ports that were too short to make sense. I like the rectangular ports, but I was trying to avoid making a long narrow slot that is supposed to be more prone to standing wave issues. The round ports seemed safer and easier to tweak/tune for my modified design.