[Brightcolours]

The STF acts as a gradual aperture. Lets assume (for ease) the lens is an ideal T2.8 lens without the STF element. It loses a whole 2 stops over the entire "frame". To get to T5.6, Some of the "gradual" aperture must be smaller than f5.6. So you get a percentage of light that acts as if it is diffracted through an f8 or smaller aperture (maybe even f22?), all the way up to f2.8.

 

The STF or apodization element sits comfortably far away from the aperture:



This will mean even stopped down this element will act as "gradual aperture" and add extra diffraction softening to the image.

 

Also, since this "gradual aperture" sits further away than an aperture normally would for a normal 100mm f2.8 lens (I am assuming that the actual aperture sits in the open gap between the 4th and 5th element, from the right), the diffracted light travels further and spreads out more at the image plane than you are used to. "Gradual aperture" distance-wise it is as if you test a longer lens (say 135mm, 2.8 / 100 * 135 = f3.78), and then you still need to add the gradual part. So lets say 5.6 / 100 * 135 = f7.56 on average for the light that passes through the STF element .