Greentea uses USBTX and USBRX to create a serial port regardless of USBDEVICE. It only checks for DEVICE_SERIAL.
Besides, it doesn’t seem right to have to ‘remove’ all USB devices just because I don’t support UART over USB on my board. More so because the same GreenteaSerial class which uses the USBTX and USBRX definitions for the transmit and receive pin, uses the STDIO_UART_RTS and STDIO_UART_CTS defines for flow control!
So I did settle on adding "USBTX=NC" and "USBRX=NC" in the "macro_add" portion of my custom_target.json. But it remains weird to have to explicitly mention that there is no serial over USB.