Thank you spyhunter99 for your reply.
I am not sure I fully understood what you mean. Are you saying that JAXWSProperties.SSL_SOCKET_FACTORY is used by JBossWS-native but not for the transport layer as it is JAX-WS RI/metro?
Rebuilding JBossWS-native isn't really something I would like to do trying to build an portable JEE application. However, I have done some more searching on the issue and found out that it is possible to achieve the same functionality as in JAX-WS RI by switching to JBossWS-cxf and use some custom code to set the TlsSettings. Not optimal as it would require the Apache CXF at compile-time and I would have to check if it is available at runtime as it will not be when running on GlassFish but anyway.