A really nice feature for transcribing games is the ability to insert forgotten moves. When entering a game that was played offline, if you forget a forcing exchange and only notice after adding in 50 more moves before noticing it’s a pain to have to redo it all. KGS/Cgoban handles this by allowing you to make the correct moves in a variation, and then cut/paste the rest of the mainline onto the variation.
Another common use case is you put a few moves in the wrong order. A similar cut/paste solution works here too.