"If the LED on the board is still red". Do you mean the D1 on S32K144EVB?
If so, the reset signal of MCU may be low(You can measure it by using oscilloscope). Which mean the project may not run at all.
S32K144EVB D1.png
After flash MCSPTE1AK144_BLDC_6Step demo to S32K144EVB, the D1 LED does not light.
Step 2 Program Base Board
DEVKIT-MOTORGD_QSG Step by Step.png
And I am able to connect it in FreeMaster.
I don't have DEVKIT MOTORGD board, so just power S32K144EVB by OpenSDA J7.
FreeMaster Probing UART Ports.png
Due to the definition of J107 is different, please check the SCH version of S32K144EVB. So that you can "make sure base board is configured to be powered externally".
DEVKIT-MOTORGD_QSG J107.png
J107 P5V_SBC.png