seelindarun,
I think you would have to alter the internal numbers to fool the game into thinking that the alternate skins set to the s1, s2,s3,or s4 values were stock skins for the townies to use them... I'm not sure what that would do, actually. I've heard that by changing the creator # in SimPE to all zeros that the game will remove the '*' symbol, but with skins there are only 4 main icons and without the custom flag those skins might not show.
Eyes should work the same. Set the creator number to all zeros in addition to the genetic tag. They should still show up as options for CAS because there are more icons open for eyes.
This is all theory, and I could be way off base.
Eh... check genesims! Madam, hats off to you, I didn't even know you'd cracked this open.
An easier way would be to custom make your townies by making sims and then using the teleporter shrub to set them as townies.
I've made townie-friendly skins, but they don't show up in CAS/BodyShop. Now, someone over on MTS2 (wes_h?) figured out how to make a new collar show up in create-a-pet, and there may be a way to use that information to make townie-friendly skins show up with icons in BodyShop. However, I think we can all see how that is a new and terrible power that would probably explode your game. Or at least your interface.
What I ended up doing is just exporting/importing the skins I wanted in BodyShop. I then cracked open SimPE, set the creator to all zeros and set the genetics. As a result, I ended up with two skin files. One that I could select in CAS/BodyShop, and one that the game could select when spawning.
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I haven't tested it with anything higher (more recessive) than 5, or decimals out more than 2 places, but even if I inadvertently worked within game constraints, that's at least 600 different genetic values to play with.