Linux software from the repositories doesn't need to ask for permission for anything (except sudo). Still, there is no malware in the repositories, at all. I admit I am a little bit vague on how this works too, perhaps I'm missing something obvious, but how do they do that?
You are simply trusting whoever is running the repository, most of the time this the distro itself, which you already trust.
You are simply trusting whoever is running the repository, most of the time this the distro itself, which you already trust.