For single pulse with eMIOS there are two ways, using DAOC or OPWMB mode.
Please find attached projects.
In DAOC mode, pulse width will be defined by duty cycle and it will enter to the ISR once.

In OPWMB mode, it will be necessary an extra GPIO output, pulse width will be defined by period and it will enter to the ISR twice.

If you need continuous pulses, comment "#define Single_Pulse" line.
Please use S32DS 3.6 and RTD 5.0.0 with S32K31XEVB-Q100. If you need an different S32K3 derivative, you can create a new project, do manual config and code copy.