ATMega1284p new chip fuse selections in AVR Studio 4.13

I didn't know [JTAG] was available to with Arduino.

It isn't "available." But it is "possible." You would have to use a debugger other than the arduino IDE, an add-on JTAG device, and some sort of kludge to get the jtag signals from their pins to the standard JTAG connector.

JTAG is also possible on the arduino MEGA boards. The fact that you don't hear of more people trying to get it working is an interesting contrast to the frequent complaints of "no debugging support."