Er, "best case" you end up creating a better version of the thing. We are on HN where you always see "Rewrite from scratch in rust, go,..." or "Version 3.0 drops backward compatibility and greatly improves ....".
After multiple decades large agencies probably need big reforms. If you can implement these within the agency, great. If not, splitting off some of the work to a new agency with these changes is a practical option.
You cannot simply reenact the same policies in a different organization and not get the same problems. Politically, you have to start over on many established political policies. While there would be an opportunity to split the org chart, then introduce new shortcuts and workarounds to the previous implementation, you just restart the same divisive issues with new contexts.
This approach makes no sense to start on. You want an overhaul of FDA policies, then advocate for that unless you have some plan other than throw everything away and let someone else deal with the practicalities.
Things used to get overhauled more regularly. The last however was probably 20 years ago with the creation of the Department of Homeland Security. Since then, crickets.
Deconstructing a necessary regulatory agency isn't the solution.
Best case, you end up creating a worse version of the same thing.