Each pad contains ESD diodes to ground and Vcc. If you have the chip powered off, you'll need <1V to enable these diodes to Vcc and you'll be phantom powering your circuit.
If you have the circuit turned on you'd need Vcc+ <1 Volts to do so. If you have two multimeters, measure the voltage of the other one in Ohms mode.
If you measure 6 Mega Ohms (both ways?) between GND and UGND it is a "isolated" ground for the USB driver stage.
USB consumes a huge amount of silicon area because of the line capacitance it is required to drive.
Atmel seems to have chosen for a separate ground for this area reducing in-chip currents. I would guess other manufactures do this too, but do not label the pin differently.
That jumper is a mystery. It is probably there to be able to measure current in the development stage.
You can always ask Atmel for more details. They cannot put everything in their datasheets.