I am happy to report success, here is Jax sporting his
fixed alien eyes. The problem is all down to EAxis and how they are generating the customPart TXMT data in the character files. The teenage aliens and normal skintone sims are missing some vital data so they don't use the alien eye texture at all. I fixed it by hand in SimPE for a normal skintone as follows:
for each customPart txmt definition:
On the Properties tab:Change baseTexture1 to baseTexture2
Add a new baseTexture1 with the value uuface-eye-alien (NB add creates a blank entry at the bottom of the list, once you have set the values, click the sort list button)
in compositeBaseTextureName: insert _uuface_eye_alien after the face txmt definition
e.g. I changed _tmface_s4_uuface_browcombed_black-diffuse to _tmface_s4
_uuface_eye_alien_uuface_browcombed_black-diffuse
change numTexturesToComposite from 2 to 3 (this will use baseTexture0, baseTexture1 and baseTexture2, adding in the alien eye texture)
On the File List tab:insert _uuface_eye_alien as per the compositeBaseTextureName value
e.g. I changed _tmface_s4_uuface_browcombed_black-diffuse to _tmface_s4
_uuface_eye_alien_uuface_browcombed_black-diffuse
For sims with alien skintones, you only need to patch the teenage customPart TXMT (paramAge 2)