I believe you are right that the pix folder would apply to the entire theme Chris.
There might be a work around depending on how the icons are created/added.
You may be able to target (some) icons with a display:none (for example the forum icons in the navigation on this site might be targeted with something like img[title="Forum"] {display:none;}. You would then have to find a way to add the new icon in your preset, possibly as something like (continuing the same example) a[title="Forum"]::before {css to add the new icon as a background image here}. You might also need some padding to give the icon some space having put a display:none on the original image.
I haven't tested this, but I think it would work - I've done something similar in the past (courtesy of work previously done by Gareth) when I was replacing image icons with fontawesome ones in a theme.
Richard