The $110 UDOO Dual core is most comparable to : RPi x 2 + Arduino DUE = $130 (using your numbers)
The $130 UDOO Quad core is most comparable to : RPi x 4 + Arduino DUE = $210
So yes, if you're just going to compare one embedded board to another, without taking into account their relative capabilities, the UDOO is more expensive. If instead, you compared the boards based on BOTH cost AND capabilities, things look very different.
Sure, for some things an Arduino mini is going to be plenty. But some projects make more sense with a multicore system processor and an I/O subprocessor.