Hi,
You can access all the register in SYSCON module without any condition, for your case, you can access the SYSCON->PDRUNCFG0 directly without any restriction.
But for exampler if you access the ADC0 register, you have to enable gated clock for ADC0
set AHBCLKCTRL0[ADC0] bit
If you want to ADC work, you have to do:
set the ADC power by configuring the PDRUNCFG0
configure the correct ADC clock with ADCCLKDIV reg and ADCCLKSEL reg.

Hope it can help you
BR
XiangJun Rong