It's an interesting idea, but I don't think it will work without code changes.

From my understanding, Lemmy federation is very heavily domain/URL dependent and already pretty finicky.

I'm not sure this works with Lemmy's current architecture unless it's fully isolated from the clearnet. When you visit a lemmy instance your browser directly loads URLs from other instances, you can easily see this with an extension like IPvFoo. Even if you hosted an instance on the darknet if it was federated with even 1 clearnet instance it would cease being anonymous.