I don't think it will let you get them separately, but if you know the aperture area, you can calculate the maximum gain for that aperture, and the CST gain will include the effect of taper and spillover, so the ratio will give you their combined efficiency. You will have to do a run with no metal or dielectric losses so that those don't contribute to a fall in efficiency, unless you know what they are. I think CST will tell you those, so you may be able to remove their effect.
You may be able to put an absorber, hole or port across the aperture and if you can do it well that will tell you what the spillover is.