I think you are spot on rocthecourse.
Just because another color would potentially give a slightly different flight pattern, doesn't mean that's a bad thing.
If players knew that blue meant understable, it would still be consistent across the molds, and we'd all be ok with buying blue overmolds, knowing that they'd fly differently. Or overstable, or light, or whatever it may be.
It's a prety well known fact that Eclipse flies differently than the black overmold. IMO, adding one more color choice for the overmold is not going to hurt the company's reputation in any way.