send AT command to Router that has microPython

is it possible to send a command ( like set D3 to High ) to a XBee3 Router that has microPython running ?
is micropython considered as transparent or API mode ?

Yes you can but it is not considered as either API mode or transparent mode. It is considered Micro Python mode.

If you are sending a remote AT command from a Node that is in API mode, it does not matter what mode the remote radio is on.

Thank you mvut , i will try this with my Xbees.
what i want to do is eliminate the need for arduino or any MCU and depnds only on remote Xbee .