The CPUs are close, but the Indy is otherwise pretty different from the N64. Totally different graphics architecture, and - relevant to getting it on MiSTer - it’s a workstation rather than a video game console, necessitating quite a bit more complexity. I’d be really surprised if it could be squeezed on.

(Though, full disclosure, I said the same thing about the N64 before the core for it came out - the folks working on MiSTer are incredible.)