The Mega 4808 can normally programmed over UPDI. The UPDI Interface is great, you need only one data wire and ground, but in some cases you wanna program the microcontroller at your board and you don´t want to make a UPDI Programmer on this board. In this cases you can use a bootloader for programming.
In most every project your microcontroller does not run all the time. You also don´t want to waste battery capacity, so you should set your microcontroller into a sleep mode.
You wanna use the Arduino serial (UART) with a Mega 4808 board? No, problem. The Mega 4808 has three serial (UART) interfaces. Here you can read on which pins you can use the serial (UART) interface and how to use it.
For testing your code for the Mega 4808 with Arduino you need a board where every pin is accesable.
You wanna use the Mega 4808 with MegaCoreX and Arduino? Then you need the standard pin usage / pinout for it.