There is no way to "mark them as such". That's half of the issue. The other half is that many people reporting these issues have not "opted into" any security tooling and don't understand its tradeoffs. They just ran `npm install`, and npm adopted default behavior of showing these warnings. For a lot of people this is their first programming environment.
>you can't automate this process, so the only alternative is to ignore all vulnerabilities.
I don't think the answer is necessarily automation. But as a package author, I'd like to be able to mark somewhere that a particular transitive vulnerabilities can't affect my users.
Or at least I'd like npm to offer a reliable way to update packages deep in the tree and override the resolved versions. Currently, there isn't such a way.