The charging circuit for the on-board super capacitor described in Power Distribution does not work as intended. It is therefore not possible to run the ATSAMV71Q21 from the on-board super capacitor. It is, however, fully possible to run the ATSAMV71Q21 in low power modes with external power connected and measure the devices power consumption trough the Current Measurement Header.
Revision 6 of SAM V71 Xplained Ultra does not have the super capacitor disconnect pin-header described in Super Capacitor.