So after a lot of googling and emailing I finally figured out how to control the RTS level (and DTR level) on linux. Through the use of a simple program setSerialSignal I can set RTS and DTR to high or low. Please see instructions and the source code here:
And just the source file here:
This works a charm and allows me to now set the RTS low at boot-up. However, there will still be a minute or so at powerup while the PC goes through system startup and the bootloader where the RTS will be high – as this appears to be done at the hardware/BIOS level. As a result, I will definitely be adding a physical switch to the RTS line so I can switch it off when it's not in use – which would be good practice anyway (but for some reason not included in the various designs).