NA's config is not in domain.xml. NA's lifecycle puts some limitations. Its vm has to start pull down(sync) the domain.xml from DAS. If DAS has a config for NA it may be too late to configure the java sys props as the VM is already in action. In any case, there is atleast one more way through startserv script in glassfish/nodeagents/<your-na-name>/agent/bin/startserv. That's when you start na using that script.
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