This basically means that if WEB-INF/classes were zipped up into a JAR and put into WEB-INF/lib, nothing would change.
Is that a bad intuition?
I would sometimes want it to work like that indeed, and it always has been surprising in a way it doesn't work like that. On the other hand, the .war is more than just WEB-INF/classes, it's all the other things in the war file too (other files in WEB-INF/ and the root of course).
Right now archive inspectors (like the one in GF) inspect the archives, and treat the WEB-INF/lib entries as embedded archives, but not WEB-INF/classes.