Yes, if you want them to panellise your boards then the panellising fee will apply.
The 5x5cm service is max, so anything < 5cm will be price X, if you want panellisation it will be price Y, I don't know what panel sizes they support off hand but I guess you order the maximum you can fit on a panel as you are essentially paying for the panel, on a 5x5 service it will be pooled probably, with panellisation depending how many you want it may or may not be.