As you see in the modern Canon charts the difference between the two lenses is about 10%points at maximum, whereas the speed of lenses varies by factor 2.
"Transmission" thus is used the way I did above.
In general transmission refers to the ratio between in/out. If more goes in (larger front lens diameter), more should come out, the ratio being unchanged.
So, basically from what goes in 85-95% must come out in modern lenses with few and coated elements.