Cole, there is no truth to the later cars using darker stripes. They were all Tyrol Blue. Sometimes rumors start when a collector, who spent big bucks getting their car restored, comes to the realization their stripes were painted the wrong color. Rather than admitting the mistake, they use the excuse, "oh, they made some like this".
Many 1969 Trans Am's were repainted and restored in the 1980's and 1990's, and there simply wasn't that much info on them at the time. Many restorers used a photo of the original 1969 Trans Am ad, which showed stripes over the spoiler, and red decals, neither of which went into production, and guessed at the color blue of the stripes. Their best guess was to chose a 1969 blue, assuming Pontiac would have used a 1969 blue (like Windward Blue), but they didn't, they used a 1967 color called Tyrol Blue.
At the Muscle Car Nationals in Chicago a couple years ago, there were several real 1969 Trans Am convertibles on display, all parked together. Interestingly, some had Cameo White paint, some had Polar White (as we know, Cameo White is correct, which has a little cream tint to it, while Polar White is pure white). Some of these cars were restored in the 1980's and 1990's, and resto shops referenced Ditzler or PPG charts, which listed Polar White as being correct for 1969 (it wasn't), so some of those super rare, million dollar cars were repainted with the incorrect white. Same goes for the stripes. There was one 1969 Trans Am ragtop there that had stripes that were much too dark. The owner thought it was correct, until he saw his car parked next to other 1969 Trans Am's. Long story short, that car is now undergoing a full re-restoration.
So I would choose Tyrol Blue for your stripes. It would great if you could post a couple pics of your Trans Am. We always like pics.