Are you talking about the FTDI connector? The UART is not RS485, which is a balanced line. It’s not even RS232, although that is closer, because the voltage is only 3.3 V.
Of course it matters which way round! Generally, you send data on the Tx pin and receive it on the Rx pin.
If you’re talking about the one from the OEM Shop and an emonTx, Tx goes to TXD and Rx goes to RXD. It’s actually the emonTx that’s wrongly labelled as it receives data from TXD on the programmer on Tx pin of the FTDI connector, which is connected on the p.c.b. to RXD (D0) on the processor, and transmits it from TXD (D1) on the pin labelled Rx on the FTDI connector to RXD on the programmer.
So the interface is capable of full duplex operation.