I'm pretty sure Seattle got the full amount for Yedlin too. The transfer fee breaks down to this:
First, if a previous owning team put in a sell-on clause that money is taken out of the fee. Second, MLS takes a cut for the money MLS spent to get the player in the league. The rest of the transfer fee is divided between MLS (1/3) and the team selling (2/3) but only up to 650k can be used as allocation money and the rest has to be used on non-player expenses. If the player is homegrown the split is 25%/75%.