After FUE you ideally need to wait for the hair growth to begin to mature. The idea of scalp pigmentation is to create the look of greater fullness to your hair. For this to be made effective it is best to see the original hair density you have, so allowing a few months for your FUE to grow. This can help to judge if some areas require greater attention to pigmentation to others and create an even look of fullness.
I typically recommend waiting at least 6 months post hair transplant before doing any SMP in either the donor or recipients sites.