1) Yes, and no. It means that the App Server must provide that functionality, whther it does so as part of the JVM or not is up to the App Server vendor. Example: Java EE 5 requires Java Util Logging; this logging is part of the JVM, whether the App Server provides funcionality around this or not is up to the vendor; JBoss AS 5.x recognizes Java Util Logging and redirects it to Log4J which performs the actual logging.
2) Yes the App Server must obey the JNDI SPI specifications. Typically, for this type of functionality, the JVM provides a rudimentary implementation that works just fine for a stand-alone app. The App Server will implement more robust funtionlaity to support multiple deployed apps and remote apps. So JBoss AS does not reply just on the JVM's JNDI implementation but rather provides its own (at least, that is my understanding- I haven't researched the JNDI code specifically, but I know, for instance, that my statements apply to RMI).