"The only real main limitation of a SB3 stock or modded is that it cannot supply an external dac higher than 24/48 where as the Transporter can do 24/96"
I can't find the passage now, and also it didnt tell how to, but there was a thread, maybe
http://forums.slimdevices.com/showthread.php?t=19822,
mentioning some advanced geeks were able to stop the SB 3 from halving 24/96 down to 24/48 on the digital outs, thus delivering full 96khz.
Haven't dug further into that yet, but since the SB primitively drops every second sample from 96, it seems there indeed could be a way to stop it from doing that. Possibly it was just decided this way to increase compatibility for older DACs?