Hello,
However, in the case where PLL is enabled in the clock configuration, the library driver provided by SPD does not set these two bits to 1.
1. Is this a design flaw or do users need to manually modify certain code?
2. If it's a design flaw, how should we fix it?
As the only validated configuration is with PLL:

I assume these bits are set in BIST precondition sequence of driver.
Otherwise you will get a STCU2 watchdog error in STCU2_ERR register as the execution wont finish in time with slower IRC clock.
Are you able to execute the test successfully?
On top of that you wont be able to debug the RUNSW register, as soon as you write 1 to run, you will loose access to the micro.
But I am not deeply familiar with SAF driver, so I cant speak for the SW team. That would require to rise ticket at NXP.com
Best regards,
Peter