I have some more info on my experience with the pricing discrepancy. About 90% of the time Shopify shows a higher discounted price for Ground Advantage compared to the 3rd parties I check (Pirate Ship & Shipping Easy, which are always identical to each other). In one case Shopify’s price was $2 higher ($15 vs $13). Usually it is < $0.50 higher for my situation. About 10% of the time, Shopify actually shows a slightly lower price.
But they always show the identical full retail price as the others, so that should mean they are calculating the new Ground Advantage retail price correctly, at least in my case (7lbs, < 1cu.ft.).
I have been in frequent contact with Shopify Support to show several examples, and so far their response is that they must just have a different calculation for their discount vs. the rest of the common alternatives. They say they are looking into this, since they have had other complaints, and they want to offer more competitive rates.
I would expect better rates, especially for the more expensive Shopify plans, which claim higher discounts on shipping as a benefit of upgrading. Not a good look when a free alternative (Pirate Ship) is often cheaper. We’ll see.