> it is a legitimate version 2

Maybe, but then the previous one was version 1, not a prototype. I've never seen people actually write prototypes, nor management accept time invested on writing prototypes, in any job I've had.

Prototypes always directly become version 1 on production, unless of course the whole project gets canceled mid-development.

I've seen rewrites introducing massive bughunts and upsetting customers without improving too much. I've also seen customers expecting and even relying on old bugs for comfort.

Rewrite is always a business decision and need legitimate reasons. You rarely have those reasons, knowledge and time between projects.

I like to remember how eBay have rewritten their backend three times.

Not because the previous version was wrong, but because it became inadequate as business grew and requirements changed.