I analyzed javassist.util.proxy.ProxyFactory and found out, that the resulting proxy is only just instanceof javassist.util.proxy.Proxy if a persistent class has a non-private method javassist.util.proxy.MethodHandler getHandler(). Otherwise it will always be instanceof javassist.util.proxy.ProxyObject.
Now the question arises, if this should even be allowed, because if not, we could replace usages of javassist.util.proxy.Proxy with javassist.util.proxy.ProxyObject again and hibernate would also be compatible with older javassist versions.