That diagram is not helpful to me (too convoluted), and I know why.
It's simply because those two pins are used for the uploading process (they're connected to the USB/TTL converter on the PCB). And whether you have to disconnect other hardware, depends on what that hardware it is. I've successfully uploaded software with stuff connected to TX and/or RX, and also ran into situations where I had to disconnect those things. It's generally better to disconnect TX and RX (and not use them as long you have any other pins available in the first place).