Well anytime you go from arrival to departure in an international airport you have to go through a transfer desk where documents are checked, security etc.

But your question regarding the redundancy of going to the check in counter when you've done it online already is a good one. Yet when I talked to Turkish Airlines in Tokyo (I called them because I live in Japan) they said I would have to check in at the regular counter in Incheon. Without bags to check in, with a self-printed boarding pass etc. -- why? Does it make sense to anyone?

My biggest worry is that because I bought the ticket via an internet agency I won't be able to check-in and/or get a boarding pass online at the Turkish Airlines website (only doable from 24hrs prior to departure). Anybody with experience with Turkish Airlines on such issues-- input is appreciated.