I also held these samples up to an 06 GT and they are MUCH different.
So you've physically put the samples to an 06 Heritage and they were very clearly not the same?
They should be the same, or very close. There's a lot of variability in the 06 Heritages from one panel to the next, but I would expect your sample to be similar. Usually if you look at an 06 Heritage under inspection lighting, the door, b-pillar and clamshell will all be very slightly different, but some have really significant differences, especially depending on environment.
If your sample is definitely *significantly* different across each panel, I would take a pic, send it to your concierge.