For programming the board, are you using our Model-Based Design Toolbox for S32K? Because with our latest release for S32K, we've added a Simulink Block call "FTM_Hall_Sensor" dedicated for this operation.
maybe not relevant, but there is similar topic discussed in this document: https://community.nxp.com/docs/DOC-340132 , but it is more related to the bare-metal (hand written C-code) approach.