The original WV Golden trout was a mutant RAINBOW...how did it becom an entirely new Pure Strain Golden if it is a mutated gene RAINBOW...later crossed with Rainbows in PA...there is no new line here...all are mutated Rainbows.
Just because they're all mutated rainbows doesn't mean they'll be the same as a rainbow genetically. I wouldn't call them a seperate species, I think they'd be better described as a subspecies or a breed of rainbows. The first example that comes to mind for a similar situation is the Jack Dempsey Cichlid, a popular, agressive aquarium fish. There is a brightly blue colored variation available a very nice looking fish but from everything I've read they're different from the standard strain beyond just color. Instead of being agressive, they're reportedly a very timid fish and very few of them make it to adulthood as they seem to be particularly susceptible to disease. Just because the golden rainbows are bred to look different doesn't mean that'll be the only way they'll be different than the rainbow. I do agree with you that that doesn't make them a different species, but I think they are a unique genetic strain of rainbow trout that is different beyond color.