I did not say two different things. PharmCAS provides an overall GPA as well as a science GPA to the schools which receive your application. They all count your overall GPA. Many put more weight into your science GPA. Either way, if they see something then it is part of your application. Seeing something is counting something.
I don't know where these kids get the idea that admissions is based purely off of statistics. Real people are on these admissions committees and everything they SEE will COUNT towards their opinion of, and therefore admission decision regarding, you...
With that being said, since it is real people reading your application, a bad year isn't the end by any means. A 3.2 GPA is just a stat to COUNT. When someone on the committee SEES that you had a 2.6 freshman, 3.0 sophomore, 3.4 Junior (and so on), it paints a picture that statistics can't. It shows that you matured and found some direction.
Let's not play semantics about what schools will COUNT and what they will SEE, because they will make a decision based off of what they think and feel about you as a person. Stats, experience, PCAT all matter. What really matters is the story the combination of these things tell and, honestly, your interview is when they really judge your character.
So no, I did not say two different things. Learn to take advice without picking it apart.