I wonder if he enjoys having such a big tail

Of course, all for science. 😏

Allow me to be a bit morbid for a second.
Even in the vanilla game this raises quite a quandary. Despite being a fusion of Bill and Nidorino and having Nidorino's body, Bill seemingly has complete control over the body. What then happened to Nidorino's consciousness? Does it just lie dormant? Is it still there but fighting a battle it can't win, Bill's mind winning out? It's kind of fucked. Imagine if someone stole your body and kept your consciousness imprisoned, unable to act, only watch, watch as your body does things you had no intention of doing.

This is the one thing I didn't want to think about, haha. For this particular instance I would say this didn't require a Nidorino sacrifice, or it was possibly a symbiotic relationship

Maybe while Bill is asleep/dormant, Nidorino is awake and vice-versa. Like a were-nido or something. Then when Bill is awake the next morning the house/lab is a goddamn mess or he's out in the middle of the forest or something with no recollection of how he got there.

That's actually kind of an adorable idea.

I feel like evolving would make the fusion permanent. He's physically a way different creature than when he got fused before so it's not like you can just throw the machine in reverse.

Better stay a pokemon forever, just to be safe ;D

I am so so happy to see fanart of one of Pokemon's neglected canon tfs (sort of), and I'm even more glad to see the direction you're taking it. I love this!