Ok - I was putzin around and I think I figured out a way to explain this in an understandable way.
Ok - I set up Sonar to record with WDM 24/96 - I wish to record a S/PDIF source thats NOT 24/96 but 20/48.
No matter if I disable Direct S/PDIF recording (set to OFF) - sonar changes the recorded wave into 24/96 - and thus, sounds like a chipmunk as well as shrinking the clip exactly in ha;f (as you might expect)
So I have concluded that there is not sample rate conversion happening when recording SPDIF sources on the LDII Optical /Coax that are NOT at 96Khz already.
I can only test with Coax on the LDII btw.
I have NO idea if it IS working in the case of Analog sources, but I can at least record with out melvin butting in.

(bad attempt at humor with the 'chipmunk reference')
I suspect few here will be able to test this, not having an A2 or an available 48Khz SPDIF source. But I will post this for the record and hope maybe it can be addressed.