Yes — based on the RA6E1 LQFP-64 datasheet, I’d group each physical pin only once by its primary/common function like this:

No pin is duplicated between groups. For pins with alternate functions, I placed them in the most common/primary group: power pins in power, oscillator pins in clock, USB data pins in USB, SWD/JTAG-capable pins in debug, and the remaining multifunction port pins in GPIO.

I’ll apply the functional pin grouping to the part symbol, keeping each physical pin in only one group.

Core groups are applied. I’m normalizing the pin type values to Flux’s standard values and tagging the remaining multifunction port pins as GPIO.

Applied the datasheet-based pin grouping to the part symbol.

Groups used:

I also normalized pin types where appropriate, and each terminal/pin was assigned to only one primary functional group.