You have to look at what games they are focusing on. All the games they see as vital for their company is made purely for PS. The fact that they release their side projects on Nintendo systems is not the core of their video game business. PS is the core business for SE, Nintendo is a bonus platform where some of their side projects can be released.Nintendo regularly publishes Square Enix games regionally, about once per year. Has Sony published any SE games in the last decade? Or any SE games period? They published Squaresoft games pre-merger and pre-EA partnership.
Publisher deals are a wildly closer relationship and larger total value than marketing deals in exchange for exclusivity windows.
I mean they don't even release most of their AA games on Switch, stuff like Star ocean the divine force and Visions of Mana.
I even think Xbox is more of a priority for them right now than Nintendo, with all the big announcement they now reguarly do with Phil Spencer and other Xbox higher ups. Makes sense, they have already announced that they will stop making the side project games they used to make for Nintendo, so now they are even more AAA PS games than they were before, so they now want to grow their relations also with Xbox more and more for their AAA only future.
Square Enix is going the same route as Capcom, and we already know that means almost no more Nintendo games, with all focus being on AAA games.