Connecting AVR Microcontroller to USB
TXD and RXD would be used if you were using the UART - that is, connecting the chip to a USB to UART (TTL) adaptor. You aren't, you're interfacing directly to USB and bit-banging the USB protocol (which is IMHO one of the nastiest things anyone could ever do on a USB bus), so you have to use the pins mandated by the software that is doing said bit-banging.

Can you get it to set registers? Sure - if you write the software (using the V-USB library) to do it.