Sometimes PiAlign "thinks" a smaller port is acceptable, sometimes it chooses a larger port. But, except in rare cases, I usually find its port suggestions are reasonable for the cabinet size suggested. The times you might choose a different port are times when port installation is difficult or sometimes when a high-excursion driver would make port turbuulence a problem at high power levels. These situations sometimes require special port placement or size considerations. It often depends on your cabinet layout and intended use. PiAlign is a software tool that I've found extremely useful, but ultimately, the design choices are still yours to make.