I think one major fundamental difference between Wilson and Portnoy is:
Portnoy looks at working with other musicians as crossing them off his bucket list of who he wants to play with. Kind of like, "I want to work with this guy or that guy because I haven't yet, and whatever music comes out of it, cool."
Wilson looks at working with other musicians as finding which guys best fit whatever project he is working on at that moment. Kind of like, "Okay, who is best suited to fit this project?"
Granted, there are exceptions, like Storm Corrosion specifically being a Wilson/Akerfeldt project where they went in having no idea what kind of music they'd come up with, but overall, I think it's usually the opposite with Wilson.
Neither approach is right or wrong, or better or worse, but it just shows the difference in how they approach projects, their completely different personalities notwithstanding.