Hello,
I cant comment on Hello world SW as I am not familiar with it.
But I can say, RM is correct. So probably example is not.
You can use our calculator to ease the work with clocks on this device:
https://community.nxp.com/t5/MPC5xxx-Knowledge-Base/Excel-MPC5744P-Clock-Configurator/ta-p/1129245
Which is aligned with reference manual.
We have also posted a ton of examples here:
https://community.nxp.com/t5/MPC5xxx-Knowledge-Base/MPC5-software-example-list/ta-p/1102445#MPC5744P
Best regards,
Peter