The diet experiment is presented as present tense. The cat smell experiment is described with “I once ran an experiment”, part of the speaker’s “thesis”, which is in the past. They are clearly keeping #42 alive to be used in totally separate research, in this fictional The Onion esque scenario.
I found a source that includes the second half which makes it more obvious:
Dr. Macho believes #42’s behavior is intentional and aimed specifically at him. “I caught him laughing at me once while I was trying to sort data he’d fucked up. I know what you’re thinking, ‘Can rats even laugh? And what would it look like?’ Trust me, when a rat laughs at you, you’ll know.”
When asked why he doesn’t simply exchange #42 for a less malicious rat, Dr. Macho explained, “You can’t just use an infinite number of lab rats. They start to think you’re a psycho if you keep asking for more.” Dr. Macho sighed. “I feel like I’m living in an annoying Pixar movie where I’m the bad guy – oh, wait….I’m the bad guy. I’m the evil scientist performing experiments on a sassy, smart rat. And my name is Dr. Stu Macho? Oof, yeah, I’m the wrong one here.”
Just behind Dr. Macho, #42 winked and walked directly into his food bowl.
