I would like to use the USB for the usual, sending commands, receiving data and programming the device. While the first 2 is possible directly through the Arduino's hardware UART RX/TX pins, programming the Arduino through just RX/TX would need like an FTDI programmer and it would not even reset whilst if we program it from USB it does them all.
The goal of this project is that the Arduino will be sitting on a PCB and I don't want to bring another extra USB cable out to it, if it would be possible to do the usb connection from the pcb as well it would be better.
Ok, yes. You can connect a USB-Serial adapter to the Rx & Tx pins and transfer data to or from the Pro Micro. You can't program it using this additional adapter, though. At least not without a special version of the bootloader that will accept new code from the additional adapter.
board cost 2-5$ and you makes yourself doubts about non existing problem that may be happen in far future?
if in your country arduino is expensive you may use such adapter placed in enclosure