Connection between Cyclone III with ATXmega or HC series logic device

If the I/O voltages match, you can connect the ATXMega and Cyclone directly.

The presence of bus transceiver and resistors on the dev kit is most likely a protection measure. If you have a dev kit that is being used for any number of things (some may use the buttons, others not), it is sensible to have series resistors in case somebody configures the FPGA pin connected to the transceiver as an output not an input - in essence to protect against damage due to bus contention (e.g. one end drives high, the other drives low).

It may be worth adding resistors between in your design as well for the same reason - protect the FPGA just in case something bad happens.