This design change to manifest V3 isn't about tampermonkey. It's about the capability space of manifest V2 allowing a malicious actor to make something like tampermonkey, have it grow in popularity, and then flip the script under the hood via the extension fetching an arbitrary script from a third-party source and executing it to turn every installed node into a botnet agent without changing any of the code in the extension itself.

Google is trying to solve a similar problem here to the one they have to solve with App Store apps: the ability to make claims about safety an end-user can trust. They can't make those claims if the extension can modify its behavior without any way for the Web Store administrators to know.