Unfortunately the real issue here is nothing other then an unqualified pilot put in the wrong place at the wrong time and a cockpit culture that prevented the more qualified PNF from immediately taking control of the situation.
At the end of the day this is not a SS vs yoke, A vs B or even an "automation" issue. In fact this appears to be one time that the automation actually worked correctly...handing off the plane to the pilot in a relatively stable configuration due to conflicting data. In effect as soon as the AP computers recognized "garbage in" they kicked the plane back to the PF in order to avoid "garbage out".
Sadly the "garbage out" was provided by the PF.....