If the head shape (the green points) looks a lot larger than the participant's head, there was probably an issue during its acquisition. Something in the room could be distorting the magnetic fields recorded by the Polhemus. You should be very suspicious about this file, and not rely much on the MEG head registration...
Do the best you can in guessing where the head was in the helmet.
Projecting the EEG electrodes on the head is a good idea.
But you can't apply anything similar to the MEG sensors: this is a rigid array and its shape does not depend on the head shape.