The RA4M1 has rather a lot of clocking options. The ARM processor is divided up into several independent modules, with clock/data synchronization as required.
The basic rule-of-thumb is that the USBFS module must remain on the 48MHz from the H0CO, the rest is up for grabs.
With the crystal fitted, all the peripheral timers etc should be driven by that so we should have much better timing-accuracy.
Which clock-source the main ICLK is derived from I am not sure yet, I need to dump the clock registers to see the settings.
Sorry to be vague, it's been a while since I have looked at this.