Hi,
Myself being new to SoX and unfamiliar with the code, my advice would be to try all three ways, then run a few tests to find any bad behavior. Trust, but verify.
file A = one call with several switches.
file B = several calls with one switch.
file C = several calls with one switch, piped together.
Null test
Invert the phase of B, combine with A, listen for problems.
Invert the phase of C, combine with A, listen for problems.
Invert the phase of C, combine with B, listen for problems.
Spectrograph
I would also load files A, B and C into spectrograph software to see what information is present at the very bottom bits of the bit depth.
Try the conversions without dither to see if the spectrographs show different levels of truncation noise.
-James