It would make sense to limit how many cover stories we invent...
but it also reduces the trouble we can get Zaiyu in when people start poking at his cover.
While it's a good idea to limit the number of cover stories, it's also pretty overwrought and unnecessarily complex. While for
most of the girls the cover sounding like it's right out of a manga actually fits their new lives as Magical Girls, their leader should pretty much hate this story. From her perspective:
Option 1- The cover story of there being a "Magical Human Tradition" that interacts with magic to some degree is true and exists . . . and they've basically left her alone to deal with her Father and the machinations of her Father this whole time. All of the hard work she (and her genius on staff) have put into . . . and there could've/should've been
support for them this whole time?! Where have they been?! What have they been doing?! They need to be
helping right freaking now because her Father is insane!! Give my team aid, please, now!
Option 2- The cover story is a lie . . . but by who and for what purpose? Investigate using Zaibatsu Heiress resources the claims that such an organization exists! Socially pressure the "agents" of this "organization" interacting with your team of magical girls to offer specific information that can be investigated! Keep forcing them to twist and turn to maintain the cover and eventually piece together a full picture of what's going on! Make sure to pressure aid out of them, see if that gives any clues!
A better cover story is a simpler cover story with less moving parts. Kai Tendo is a mysterious investigator with relatively unexplained powers that's secretive, work-oriented and living outside the human norm. Makes his money doing odd jobs but especially information gathering work, because he loves it. He often investigates magical situations for fun but he usually can't find a client. Mundane situations are
usually beneath his skill level but at least they pay. He's not talking about any specifics of his magic. He's especially not talking about any organizations full of moving parts and verifiable loose ends. He's a troubled but brilliant loner that stumbled onto a
much more serious situation than expected. An anti-social version of what happened to Miss Zaibatsu Heiress and her brilliant colleague/subordinate. They're smart, lucky/unlucky, and doing their best. Kai just has much less access to support than them.
The "lone genius stumbles into it" story is also much harder to investigate for multiple reasons. The biggest simplification offered is that there's no organization to track down or theoretically support Kai and potentially the Magical Girl Team. Impositions for assistance are asking Kai
directly to spend his time helping, which is harder to socially pressure than some nebulous organization of unknown membership and means.
There's nothing preventing him from knowing Yuu of course, but he's also not explicitly connected to Yuu in any way. Zaiyu can leave the Yuu identity to be a more mundane friend that has no reason to be involved in the magical side. Thus, there'll never be a social gathering that Yuu and Kai should both be at. This is a major flaw with having them both be in the same organization.
TL;DR the cover story of a larger organization is actually
too true for its' own good and
way easier to prod and twist at than a simpler one would be. It pins the focus of investigation onto a mysterious
group rather than focusing on the mysteries of a lone individual that could
plausibly have stumbled into the whole situation like the Heiress and the Boy-Genius did. By being so large in scope it limits Zaiyu's maneuvering room and gives the Heiress plenty of leads to pull on and/or investigate.
It's somewhat competent as a cover story, but it's not the hyper-competence Zaiyu has generally been using. It's much more aligned to the teenage part of teenage-genius than the genius part.
But it sounds like a lot of fun to try to watch Zaiyu try to make it work
