It's possible to make it so you enable it on a per mod basis, like app permissions

Because that's never ever been a total usability disaster that just encourages people to enable every one because they don't feel like fighting it. It's also not effective, given how tightly tied mods are to the core API.

When you're talking about security, adding a bunch of config flags for users is never a good idea. Most users aren't going to understand what it does, and like others mentioned, there's too many reasons to turn it on.

I see no problem. It's those people's choice to do so, and they accept the risk.