This is false on multiple levels. For a fact it is absolutely NOT "always allowed". If you ever ran a find or ls that goes into dirs like Downloads or Documents for the first time you would know you always get a prompt. But once it IS allowed, you can write there.
You're right that there is protection and verification of some signed app bundles, and I was wrong to say you can easily edit apps. For most apps even if you can edit them macos should raise a stink and say the app is damaged IF SIP is enabled and macos checks the signatures.
But I don't know if it works if the app is modified before first launch and launched without Internet because this is verified through Apple notary servers. Also I wrote files and modify plist in some signed Tauri/Deno app and spctl did show a warning but macos didn't care and launched it without any alerts.
And anyway if you have xcode set up some sus code can also sign whatever they write and good luck then;)
TL;DR as I wrote in another comment using ~/Applications is not totally insecure with SIP and all but still less secure.
This comment was edited, my original comment was too dismissive and wrong.
I can edit plists for a bunch of signed and popular apps but MOST of them would be "damaged" on next launch. However a Tauri template app was launched.
and malware doesn't need to modify apps. Just rm an app and put a modified version instead. You can do this in ~/Applications without sudo or app management permissions
Yes some dev tools like Docker ask for admin passwords, but that's not typical of most Mac users experience.
Root still exists, but outside of software originally built for Linux or some odd edge cases, you won't encounter it.