On Thu, Apr 21, 2016 at 11:07:37AM +0000, Reizer, Eyal wrote:

* (i) If the transfer isn't the last one in the message, this flag is
* used to make the chipselect briefly go inactive in the middle of the
* message.  Toggling chipselect in this way may be needed to terminate
* a chip command, letting a single spi_message perform all of group of
* chip transactions together.

Now, in my case I need the CS pin to go inactive and stay inactive during the transfer 
of the next byte for completing the SPI init correctly (sending the extra clock cycles while CS is inactive)
If I read the above correctly, CS will only briefly go inactive but will when the next byte 
is sent it will be active again.
What am I missing?

No, it changes the state.  The main use case is a brief bounce but
you can use it for other things.