It seems apple only asked the pictures be taken down. Even in the author’s own admission, they could have given him much more trouble. It seems reasonable for Apple not to give their blessing to this sort of project, both to „protect“ their customers and discourage the installation of what looks like malware on a bunch of their computers.
I guess Apple also reported the artist to the secret service, but given that he installed what appeared to be Malware on a bunch of computers, it’s not an entirely unreasonable response.
The artist probably knew that if he’d been straightforward with Apple about the project he wanted to do and asked for permission for it, rather than vaguely asking whether he can take some pictures/video, he wouldn’t have gotten permission.
In the end it seems like it mostly worked out. The artist got to do the project, and only got a little trouble for operating what many would consider a legal grey zone, and he got a buch of discussion and exposure from it.