Quote -
edited to add- and maybe my perception is wrong, but that's how i read it.

cobalt dream, she was talking about the physical eye that Olaf modeled, but that I UVd differently. (And just for the sake of saying it again, I mentioned several times I am unhappy with the way I did it, but she likes it, so I didn't change it except to fix the warping in the sclera.)

So, when the Iris and the sclera are separate UV islands, it can be a bit tedious trying to make a nice soft transition since you're texturing over different areas at once and trying to line them up.
Well that's what I got out of it at least.
Not sure about the need for transparency now that you mention it though.