Interesting hypothetical but mostly not relevant at all in this case. Details are lost making the analogy and when it comes to fair use, the details are often very important.

For example, are you changing the names of all the system calls? That will break lots of software. You have to figure out how important that is.

That's a discussion that really has no analogy in a discussion about transforming a real photograph to appear like it came from a Nintendo game like all the music on the album.

The only way it could really be worth discussing is pointing out how it is different. Your example seems like basically modifying the software for the sole purpose of evading copyright. In the Baio case, it is very clear that he's not simply making superficial changes in order to claim fair use.