Unrestrained Objects can cause or worsen accidents (e.g. phone under the brake pedal). Plus there's better integration with steering wheel controls and a closer microphone for voice control.

Phones themselves aren't a problem if used safely, such as running Android Auto (full screen app version) and having it mounted so it can hear voice commands.

The problem is that people try to jerry-rig a poor man's version using Google Maps app, a phone sitting loose in the cup holder, and no voice commands ("let me pick it up briefly to pick a route").

It is the difference between ideal usage and real world usage. Built into the vehicle gives you closer to ideal usage every single time.