Arduino Zero: No device detected. Error 4109 in AS7 but runs OK in 1.6.9

Using an Arduino.cc Zero in AS 7.0.1188:

Tools.Device Programming is able to read Target Voltage but Device signature read gives:

Severity: ERROR ComponentId: 20100 StatusCode: 1 ModuleName: TCF (TCF command: Device:startSession failed.) No device detected. Error 4109

View.Available Atmel Tools shoes the EDBG as connected and right-click redundantly updates the firmware successfully, from 3.1f to 3.1f.

However the device signature of a SAMC21 Xplained Pro can be read .

Importing the Arduino.cc blink.ino sketch, AS7 builds a Release version without errors but "Start Without Debugging" debug generates "Please select a connected tool and interface and try again." Selecting the EDBG of the Zero then "Start Without Debugging" generates "Failed to launch program. Error No device detected. Error 4109"

With Arduino.cc 1.6.9 one can burn the bootloader and also upload and run the blink program successfully.

If firmware can be uploaded successfully in AS7 then why cannot the signature be read? How to fix it?

UPDATE: Using a different Arduino.cc Zero and upgrading the firmware, gives a different error without an error number, "Unable to enter device programming mode. The read device id indicates that the connected device is an ATSAMD21G18A. Please verify device selection.", also "unexpected chip identifier".