Hello @KVK,
Thank you for posting your question on the NXP MBDT Community.
If my understanding is correct, you want to communicate with the BCC analog front-end over SPI using a variable data length for the SPI transfer. As you have described in your question, there are a couple of requirements you have to match for successful communication. I will try to resume and address some of the requirements, but in order to help you, we also need some information from your side.
1. Sending a minimum of 6 bytes on transfer.
For such a task, I would suggest using the native LPSPI instead of FlexIO. My guess here is that the CS pin needs to remain asserted as long as the transfer of the minimum 6-byte frame is performed. You could achieve this using the Continuous transfer, the Advanced option of the SPI_Config block.

When this Continuous transfer option is used if an array is sent using the LPSPI transfer block, then for the entire size of the Data TX buffer the CS pin is asserted and the transfer for a minimum of 6 bytes is performed. If the master_send array has 8 8-byte commands, then the LPSPI will send the 8-byte frame.

2. Waking up the device
For such a task it is clear that the MOSI pin needs to be controlled as the GPIO and then controlled by the SPI peripheral. This functionality could be achieved in MBDT by using some custom code in which the SOUT pin is muxed to the GPIO, controlled as required by the external chip, and then muxed back to the SPI as SOUT to be used as MOSI. In order for us to provide an example in Simulink on how to achieve that, we need to know which MOSI pin are you going to use for your prototype.

3. Usage of FlexIO vs SPI
Given the points from 1 and 2, I would recommend switching to the native LPSPI blocks and pins.
So, I would like to ask you the following questions:
1. Which SPI instance and pins are you planning to use, so that we can give you an example of how to wake up the device using the MOSI pin as you have described in the initial question?
2. Which MATLAB version are you using?
As you may already know, NXP has also a solution for the Battery Management System, and MBDT for S32K1 comes with dedicated blocks to address the NXP analog front end. For more details please have a look at this article here: https://community.nxp.com/t5/NXP-Model-Based-Design-Tools/BMS-amp-MBDT-Designing-Battery-Management-...
Regards,
Marius