Hello,
I hope all is great with you. Thank you for using the NXP communities.
You are correct, digital signals such as SPI are accessible through connectors.
In this case, as the kit uses a KL25Z MCU to communicate with FlexGUI, you need to disconnect the KL25Z in order to connect your MCU.
In this case, remove J28 and appropriate jumpers to disconnect the KL25Z MCU (see Figure 5) and connect the external MCU on J30 connector as shown in Figure 6. In addition to this change, make sure that the VDDIO voltage domain is the same on MCU side and SBC side.


I hope this information helps.
Regards,
David