Where are you reading that you have 1/2 the recording time with spdif as you would when using 1/4"?
Reason I ask is because if I go into the Record Settings and choose 1/4"/16/48,and then, still within Record Settings, scroll down to Rec Time Available, I have 03:01:50 total time on media, with a 2GB card.
If I choose spdif/16/AUTO, then check Rec Time Remaining, I have 1:30:38 total time on media.
HOWEVER, if I leave it set to spdif/16/AUTO, then plug in a coax cable into the spdif input, send it a 48k signal, and start recording, I am told on the main recording screen that I have 2:53:11 time remaining on a 2GB card.
If I set it to 1/4"/16/48 then plug 1/4" TRS cables in, and start recording, I am told on the main recording screen that I have 2:53:36 time remaining on a 2GB card.