@rmackay9 You can see from here in the log:
[D] at C:\projects\qgroundcontrol\src\Vehicle\Vehicle.cc:1318 - ""Vehicle does not support Mavlink 2.0""
That the capability bits are reporting that Mavlink V2 is not supported. This means QGC does not switch the link to V2. So nothing QGC can do from that point on with fence/rally.