Note that the EK-RA4M1 devboard has a Segger debug chip on it as well, so it is easy to pop on the Arduino Minima bootloader and run code on the board from the Arduino IDE.
This then gives one the full debug capability of using a Segger device, the main difference is that under e2studio the registers are fully named, whereas running the Segger Jlink software separately the registers are generic.
The main difference to the Minima is that the dev-board runs at 3.3V, not 5V, and also it has both crystals fitted.
The price is very good too, being a similar price to an Arduino DUE.