I will now show my ignorance, so apologises up front.
My thought was that Samsung and the other SEP holders negociated by saying - Hey Samsing, Nokia here, you need my patents and I need yours, lets tally up. Right, You owe me 50c/ we owe you 50c. If that is what happens I can understand the 2.5% of retail cost that Samung is demanding. The conversation goes something like this;
Apple: We want to use your stuff Samsung.
Samsung: Okay Apple what SEP patents do you have we need?
Apple: erm well None...........
Samsing: Ah right, okay so we have nothing to trade on SEP, I guess we will need to charge you the full fee.......
So I guess if Apple had SEP patents it would help them a bit..............
Am I missing something here?