@mtm81 Thanks for the replies up to this point - I'm pleased to say that I've got it fixed (well kind of).

With my previous setup I've confirmed that the ALL of the default settings I was putting into the pi (alsamixer, retropi config, config.txt, autorun, even going so far in the config.txt to turn off the HDMI audio all together etc) to force it to use headphones - all were working but ONLY after a certain point in the boot sequence. Up to that point, because I had the HDMI plugged in (for video only) the system was detecting that HDMI connection and setting the ouput audio to be HDMI. Once one the files config files was THEN loaded, the Headphone output would then take over.
The issue was always that, my file which was being used to control the audio volume output of the device - was being loaded BEFORE those other files took over, meaning my file was effectively turning the volume up and down on an output I wasn't using.

I've therefore changed my output to HMDI for audio output as well, and changed my cabling from using the headphone jack on the PI, to the output jack on the HDMI controller.
This works absolutely fine and works first time.

So although this issue is solved, the underlying reason still remains - if you want to use the headphone output for audio - that only is 'forced' so far into the boot sequence.

Can't change volume in EmulationStation from a script