That is not true if you're using code signing. If someone compromises the server, they can overwrite the files, but they cannot forge code signing without additional access to code signing private keys.

Security is achieved through layers. No single layer can protect you from everything, but we lay down the gauntlet in the hopes that an attacker will encounter a road block that they cannot pass.

Exactly. That's why I'm advocating for a signed JavaScript/HTML/webapp standard of some sort.