The most important differences are:
1) The AR typically has pins 12-25 connected directly to ground, while one of those pins is an output on the PC parallel port. Outputs attempting to drive a direct ground or Vcc connection can easily sink or source harmful amounts of current.
2) A Comms Link port has an "acknowledge" input that is connected, among other places, directly to the gate control of its output latch. This allows the AR to perform instant bus turnaround (reversing the data transfer direction from PC->AR to AR->PC), and therefore the AR/comms protocol has no stage that allows the PC side to delay bus turnaround - the AR can turn around the bus at any time after the PC has signaled a valid PC->AR byte. Since this is performed with a direct control connection, even causing an interrupt and having the ISR set the port to input mode by connecting this output to the parallel port's /ACK line would still leave a window in which both devices could be attempting to drive the bus. As above, this could cause excessive amounts of current to flow in the connection.
Personally, I think the Free Wing interface is overkill for modern parallel ports (I'd prefer a simpler EPP-friendly interface), but it's well-tested, well-supported, works on new and old ports, and beats the crap out of paying to have a Comms Link card shipped from Hong Kong. 🙂