To the best of my knowledge, you can either use the Arduino C++ IDE to compile and upload programs to the board, OR install the Micropython interpreter. You cannot do both at the same time.
https://docs.arduino.cc/tutorials/giga-r1-wifi/giga-micropython/
One installed, MicroPython uses its own method to upload python scripts to the board. If you are using an IDE like for example Thonny, this will make its own serial connection with the board. An attempt to make another connection at the same time from, say, the Arduino IDE will find the port already busy and fail to connect.