I'm unfamiliar with the differences, but it sounds like getSystemSocketFactory() pays attention to system props and the other ignores them. The question for me is whether or not getSystemSocketFactory() will actually fall back to using  "the standard JSSE trust material (<code>cacerts</code> file in the security properties directory)." 
Was proving this out part of the dev testing @adreghiciu undertook, as this use case doesn't appear represented in the IT?