There is a famous picture of Rav Aharon Kotler ZTL and the Rav sitting together. I doubt Rav Aharon Kotler would let himself be seated next to someone he felt was an apikores. That is not to say that Rav Aharon Kotler ZT”L held of YU. On the contrary. Making of a Gadol mentions how he was upset as his cousin, Rav Ruderman ZT”L, for allowing college in Ner Yisroel.
I was told that the Rav was supposed to speak at the levaya or sheloshim for Rav Aharon ZT”L but was prevented from doing so. Clearly the Rav held of Rav Aharon ZT”L in high esteem, even if he felt that America wouldn’t tolerate the traditional Orthodoxy of his grandfather Rav Chaim Brisker ZT”L.
Charn is correct in his characterization of YU in its early days. Making of a Gadol mentions how Rav Shimon Shop ZT”L finished his shiur 5 minutes early and let his student out, for which he was subjected to a berating by the YU administration.