You're grasping for excuses. There are security issues with running any app on your phone. A maps app could do nefarious things with your location. A browser app could do nefarious things with your browse history. That doesn't mean Apple blocks all third party apps.

If I trust a phone app enough to use its dialer, I should be able to route all calls through it. If I trust a maps app enough to use it manually, I should be able to set it to open for all address links. It really is that simple.