Now that I look at the app note for the AtXmega again, they are doing a different thing than with the Atmega. The PDI interface is 2-wire, not 3-wire.
They have PDI_DATA and PDI_CLK instead of SCK, PDI and PDO.
On those chips PDI_DATA is a bi-directional interface, connected via a couple of resistors. See the app note AVR1612 (doc8282.pdf) which mentions connecting TxD and RxD both to the PDI_DATA pin via a 220R resistor in series (each). Like this:
Clearly this is different to the normal SPI interface.
It's a rather confusing naming of two different interfaces with the same name "PDI".