Actually, the issue is probably more to do with classloading. GemFire is, in large part, a singleton cache. Having the gemfire.jar in the system classloader means that all webapps can access sessions in the cache which is why you can do what you tried. However, if you try and access an object, placed by webapp A, using webapp B, that object would have been loaded by the classloader of webapp A and would be (mostly) unusable by webapp B.
If I understand your second approach, you're using separate JVMs to host your apps. I would imagine, however, that if you switch from A to B you would see your changes in B, but if you then make changes in B you won't see them in A. To achieve that, you would need to either use peer-to-peer mode or, if using client-server, you need to disable the local cache such that session objects are pulled from the backend servers for every request.
--Jens