It it better to trim prior to trifolding as the build up of material on the folds during guillotine operation means extra time spent aligning the pile for trimming. Also the baggyness of the middle area (between the side folds) may tear the fibres in the material rather than cut clean if the knive is dull.
Also one tip I have for trifolding is to leave the cover slightly wider (fold to edge) then the middle section (approx 1/32" or 0.5mm) to enable the end user to open the document easier.