ISE sets some default parameters for SPI mode if CONFIG_MODE is not specified in the design.
As a result, using the bit file generated in ISE with default bitstream settings in Vivado to generate a BPIX16 MCS file gives the following error:
It is recommended to regenerate the bit file in Vivado.
However, if you do not want to upgrade the complete design to Vivado, you can manually edit the .ut file in the ISE project to remove all SPI related bitstream settings.
Then run the bitgen command on the manually edited .ut file.
bitgen -f edited.ut test.ncd