I've had the same issue ever since I started with Reason+Record Duo. no matter what I do with Neptune, I can't get transparent sounding results.
actually, now that I'm listening to it again, even that second tutorial doesn't sound transparent at all. Neptune is great for voice synth stuff and messing around with formants, but it's not useful for me to get a natural sounding vocal.
although it was initially pretty frustrating, this limitation has encouraged me to push myself to become a better singer, so I'm okay with it.
if you manage to get some decent transparent results out of it though, I'd love to know how you were able to achieve them!