Company owned devices options for system apps
My interpretation of https://support.google.com/a/answer/7292363 is that
com.android.phone is a system app that cannot be disallowed
However you can create a policy which will prevent non-emergency calls:

4.24. System radio management
4.24.5. IT admins can configure whether the device can make outgoing phone calls, excluding emergency calls (see outGoingCallsDisabled).

At which point you can put your own Phone app on the device. Note limitations on Phone apps that developers are bound to.
So presumably the device will still have the Google phone app but that app can only be used to call emergency services.