Develop Software for Microchip ARM Controller in MPLABX?
Here the answer from microchip:

MPLAB X IDE v5.05 has beta support for 16 SAM devices.
These are the devices that are currently beta supported under MPLAB X 
IDE v5.05:

ATSAMV71Q21
ATSAMS70Q21B
ATSAMS70Q20B
ATSAMS70N21B
ATSAMS70N20B
ATSAMS70J21B
ATSAMS70J20B
ATSAME70Q21B
ATSAME70Q20B
ATSAME70N21B
ATSAME70N20B
ATSAME70J21B
ATSAME70J20B
ATSAMD21J18A
ATSAMD20J18
ATSAMC21N18A


Please continue using Atmel Studio for SAM Devices, till MPLAB X doesn't 
fully support the ARM devices.
More details about the Atmel Studio ecosystem cab be found here: 
http://www.microchip.com/mplab/avr-support