We got a response from Digi sw support as follows:
"Regarding GCDR, it looks like BIOSLIB/StdBios.c calls _getDoublerSetting() in BIOSLIB/CPUPARAM.LIB to get the starting value for GCDR. During startup, it measures clock speed to calculate the proper value for GCDR. The customer could hard-code a value in _getDoublerSetting() if necessary.
If they want to change the clock speed of the module for some reason, they might want to set PLL_DEFAULT_PLL_SPEED_MHz in their project settings. The default is a value of 325 which corresponds to a CPU speed of 162.5 MHz (PLL / 2)."
We used this based on the example:
printf("Startup CPU freq = %ld\n", get_cpu_frequency());
clkdbl = (GCDRShadow & 0x1F) != 0;
printf(" - initial clock doubler is %s\n", clkdbl ? "ON" : "OFF");
printf("b. div4, doubler OFF: CPU freq = %ld\n\n", sf = get_cpu_frequency());