Whereas my thought (bear in mind, I haven't played in a LONG LONG time) was that ITTWY took away the points from the MISSION, not from other sources that may have only procced off a mission. If I were to write down points every time I scored them and their source, this is what I would write.
+40 - Espionage Mission
+5 - James T. Kirk
+5 - Assign Mission Specialists
So I would have looked at it as only 40 points came from the mission, the other 10 are just bonus points. Because it does seem a little odd to me to say "Okay, I get 50 Mission points, but only 40 count towards the Intermix rule" instead of "40 Mission points, 10 bonus points."
Edit - was asking a friend who ALSO hasn't played in a long time, and he asked 'What about acquiring Ressikan Flute there? I only got it because I solved a mission, after all. Or what about Drought Tree?' as other anomalies if ITTWY hit all points that would not have been obtained but for solving that mission.