R’ Shach did not say that someone who goes to college is an apikores, he said that all colleges teach apikorsus.
If you do not accept what they say, you are not an apikores.
Thus there would be no reason to consider their wine stam yeinam.
On the other hand, if some one believes something that is apikorsus, even if he is sitting in a beis medrash, he would be an apikores.
The point was not made at all.
One who does not believe in brias haolam and believes that man comes from apes, or some similar theory, he is an apikores.
He is an apikorus because if his belief, not because he heard it.