5V GPIO is something the Uno line has historically had since the very beginning (and an assumption of having it is baked into thousands of getting started with Arduino books and guides) and I suspect using the RA4M1 is to help keep this capability.
Logic level converters are HARD. You basically need to rebuild internal structure of GPIO external to the MCU. It needs to support high speed, high current, input or output, open-drain/open-collector, customizable resistor pull-up/down.... All external to the MCU.
