I suspect issues with the present raspberry pi image and discrepancies in the documentation.
What would be helpful is a simple review of installing mopidy instructions onto a pi 3.
Assumptions:
The pulseaudio will be configured as a service rather then as a user.
Mycroft with mopidy and the mycroft skill installed.
Mycroft to be a service and mopidy to be a service.
The linux user mycroft, pi, mopidy will be allowed to communicate to the pulseaudio.
The audio output will be the 3.5mm audio jack (nothing fancy)
The mic in will be a usb connect.