Arduino IDE direct interface to serial bootloader?

On both the Uno and Mega 2560 boards, there is an ATmega16 that handles USB-to-serial translation for programming the application processor via the bootloader/UART. I would like to know if the extra ATmega16 is required. If I designed a board that was intended to directly interface the PC UART (obviously down-converted to TTL levels) to the bootloader UART, would the Arduino IDE be able to handle this without the extra step of USB-to-serial translation? Are there any additional steps required to do this?

Thank you for your time.

Sure. But most folks don't have serial ports anymore, so USB is easier.

Are there any additional steps required to do this?

You’d have to connect Arduino ground to the ground used by your PC’s UART, as well as connecting the Rx and Tx lines. Obviously you will also need to ensure that the Arduino’s power supply and the PC ground are at the same level. They probably will be, but if you end up in a situation where they aren’t then your ground connection would be trying to pull the two power supplies to the same level which is unlikely to end well.