Yes, the Serial IrDa *CAN* be connected to an FTDI cable!
We tested it out and used the Arduino Serial Monitor interface to send/receive data to a Cosmoneer. We've since updated the IrDa spec sheet to include simple wiring instructions (shown below).
FTDI to IrDa
GND - - - - - - - - - - > GND
VCC - - - - - - - - - - > +5v
TXD - - - - - - - - - - > TX
RXD < - - - - - - - - - - RX
Note: Jumper from ENABLE to +5v (suggest using a 3.3k, 4.7k or 10k resistor)