Eventually, my board becomes a "independent board".

It consists of

• FTDI FT2232D Dual USB-UART interface.
• Atmega88PA, working as jtag-UPDI interface
• Atmega4809 , the main MCU
• OLED display connected through SPI to Atmega4809

Not always FT2232D-Atmega88PA connection is not necessary, and its connection can be selected ATmega88PA or UART1 of Atmega4809. The other UART of FT2232D is always connected to UART0 of Atmega4809.

By the proper jumper setting, one of UART of FT2232D is connected to Atmega88PA and direct binary upload is enabled by avrdude as follows:

This implementation of jtagupdi is made by ElTangas, the same author as STK500 UPDI interface implementation. By the sake of this great implementation, now it's very close to be "Arduino-like" board. Currently binary is made by Atmel ICE and .hex file is uploaded by avrdude. The modified avrdude.conf is also included in the ElTangas's GitHub.