Enlighten me. 

I know that Sega is the overcompany to Atlus, but what exactly is their relationship? I mean you can see influence from one seep into the other over time (Activision-Blizzard), and then you have stuff that is more independent. 

...Though I'll admit this question started with the simple thought of 'Does Sega have the ability to make Atlus port Persona 5 to the Switch'.

They don't really tell Atlus what to do a good chunk of the time. Atlus just sees Persona doing a better job on Sony systems.

Not sure why this has to only be related to just Nintendo. What about PC and Xbox as well?.

Sega simply owns Atlus. As stated by Atlus after the acquisition (I'm stating this from my memory since its been a while, but the point is very clear for you to comprehend), Atlus will continue doing what Atlus does before joining Sega.

Once I read the title, I knew what it was leading to.

Because I am a Nintendo player and not a Xbox or PC player (plus with how many emulators and worse are on PC, what do they have to complain about such things?)

Well yes, we know this, and I can see your topics slowly being obviously geared towards Nintendo themed discussion. I just sought to break that mold with including others into the topic, since I think it makes for a more interesting topic.

Yes, it would be nice to natively play said games on my rig, rather than having to emulate them. Also, what do you mean by "and worse"?.

It depends on what do you mean by Sega. There is SEGA which is a game publisher and SEGA Sammy Holding which is a parent company of both SEGA and Altus. So, actually SEGA a game publisher has 0 control over Atlus if that’s what you mean.

Sega itself keeps certain games exclusive to PS4, like Project Sakura Wars.

Sega owns Atlus. If Sega told them to do something likke the P5 Switch port, they would have to do it. But Sega mostly leaves Atlus to do as they please, so whatever reason P5 is not multiplat is on them.

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.