Their power level is somewhere between "over 9000" and "unlimited power."

Sega is they wanted to can control Atlus as much as they choose too. They just choose to leave it acting on its own cause they're confident in their ability to make their own decisions + if they don't get involved they don't have to waste time and resources managing the company themselves. Thats all there is to it. They give Atlus control, if Atlus messes up badly though Sega would take the reigns, as is often the case with these type of acquisitions.

Think of it as how Sony deal with its studios. They have total control because they own 100% of those companies/studios, but they trust the dev and allow them to do what they want (and the results are really very showing of this working).

I never liked exclusivity, so I want Atlus to put their games on all systems. Persona 5 on PC, Switch, and Xbox One would be great. Atlus has no benefit keeping it exclusive. What would they gain by making it multiplatform?

-More people have the option to play it on their preferred platform 
-Expanding the Persona fanbase beyond just Playstation
-More revenue

Atlus has nothing to gain keeping it exclusive. 

I'd like a Switch port too, simply for the ability to play it on the go. But damn, just get a PS4 already.

I didn't know this was still a thing. The Switch is getting a Persona game. Just not a mainline one. It's still getting SMTV. That's exclusive to Switch.

This is pretty much it. Sega COULD dictate they release it multiplat, but they are allowing Atlus to function mostly independently, because there's no reason to interfere with what is working.

Shin Megami Tensei is more "mainline" than Persona, though the Persona games do seem to be bigger projects these days.

I believe porting is often outsourced to another company. I figure Sega could make that happen if they wanted to. In fact, I wouldn't be surprised if that is happening right now, but even porting takes time. It might be happening, but they wouldn't tell us til the release date is near.

Atlus probably decides on Persona's exclusivity (or potential multiplat) as much as they decide Shin Megami Tensei's exclusivity (or potential multiplat).

Though it does beg the question, what are the big Japanese studios doing at this time in regards to the Nintendo Switch?