Just as a follow up for those with interest in this issue it appears that the process described in the S6B manual for forcing the unit into SPI mode works for the through hole device, but not the SMT version. Digi Support responds,
"It looks like putting the SMT version in SPI mode with the [DOUT] pin does not disable the UART (P3=0, P4=0.) With the UART active the module discards API messages at boot. I am submiting this to engineering as a possible bug.
Digi Technical Support"
This may work in the future!