Coincidentally, one of my leagues just posted its "Top Tools: Best Pitches" today, and here are the way it ranks:
1)
Player Profile: Pete Servais: 98-82-56-63-40 = 339 /5 = 67.8
2)
Player Profile: Graham Ellis: 92-81-62-60 = 295 /4 = 73.75
3)
Player Profile: Glendon Gload: 91-76-74 (relevant to this discussion, formerly had a 4th pitch of 24 but it was dropped) = 241 /3 = 80.333
4)
Player Profile: Vic Marin: 95-72-63 = 230 /3 = 76.666
5)
Player Profile: Bonk Bolling: 83-96-43-63-49 = 334 /5 = 66.8
[side note, top NL guy was
Player Profile: Jeremy Oeltjen: 92-96-48-65-53 = 354 /5 = 70.8 which is very very high for a 5-pitch pitcher, and that's reflected in one of the lowest ISO power and lowest HR rates you're going to see on here, that's HOF caliber production]
So we see that even though Gload and Marin have a higher raw average, it somehow matters that they have "only" 3 pitches instead of 5. Also notice that there's never any 2-pitch pitchers on this list. It's somehow weighting the value of having more pitches and scaling it accordingly
Bring it back around to
Player Profile: Timothy Carreon, 82-75-52-45-4 = 258 /5 = 51.6 versus 254 /4 = 63.5. The 4-pitch version of Carreon would be scaled higher towards the top 5 tools than his 5-pitch version. So yes in a sense it matters, and it hurts pitchers whenever their end-most pitch is well-below par