Preferring Soundgarden and STP wasn't some sort of academic decision, I was fourteen or so at the time and just listened to the bands I liked more.
By the time Pearl Jam branched out more I was over the sound and mostly listening to Brit-pop.
Since those bands all knew each other and grew up together, the grunge label sort of made sense for them and projects like Mudhoney, Temple of the Dog, Mother Love Bone etc. It was lumping Nirvana in there that always seemed a bit out of place.