Setting aside whether they want her living in their sign, if they know that she's there and let her stay, I'm pretty sure that they have liability if there are problems. She was living on the roof of a building, no obvious way up or down, and if they say "sure, go ahead and stay" and she is climbing off the roof one night and falls, that's on them. Not to mention that I am pretty confident that a store-roof-sign is gonna violate a long list of code requirements for legal housing, from insulation to having a bathroom.

And even if you're gung-ho on the concept of relaxing liability and code for property owners who don't charge or something like that because you want a lower bar for homeless shelters or something, I am almost certain that the kind of place that they're gonna aim to permit isn't gonna be people living on a roof in a sign.

EDIT: Also, while I don't know the specifics of this store, it's apparently in a shopping center (and the article referenced that she may have climbed up from other commercial buildings, so they're probably adjoining). I think that the way those work is that the stores don't normally own their individual properties, but that they lease from a property owner who owns the strip mall or shopping center, and it's not like the store can just go start treating the property as residential even if it wants to, even aside from zoning restrictions from the municipality.

Lemme check Google Maps.

Yeah, it's the "Northwest Plaza" shopping center. Looks like they share a building with a pet food store and a UPS store and such, and there are other buildings in the shopping center.

https://www.google.com/maps/place/Family+Fare+Supermarket/@43.6425233,-84.2512005,215m/data=!3m1!1e3!4m6!3m5!1s0x8823d55dddb15c93:0xaf14d039d2268031!8m2!3d43.6427161!4d-84.2508454!16s%2Fg%2F11cky3vyyq?entry=ttu

Yeah, and at Street View level, you can see that there are more businesses in the same building. Like, a buffet restaurant, a pharmacy, etc.

Like, setting aside the whole question of whether society should subsidize more housing, this just isn't somewhere that it makes a lot of sense to put someone, even if that's the aim.