In addition to what Deimos have already said... "Transfer" involves a change of carrier, unlike "Transit". And with the exception of some airlines with close alliance or partnership, like Northwest with KLM, one often cannot get the boarding pass for the 2nd leg when checking in for the 1st leg. That's when most people use the transfer desk.

For example, I flew HKG-NRT (CX) and NRT-IAH (CO) in January. While my bags are transferred automatically at NRT, I need to go to CO's transfer desk at Narita Terminal 2 to get by boarding pass for the CO flight.