I didn't say the markups were available on a per-item basis, I said you could see which stores were marked up and which ones weren't. Just click on the store dropdown, and you'll see this:
http://i.imgur.com/KElc00R.png
We'd rather not mark anything up at all, and if something is marked up, we'd prefer to tell you by how much, but we can't do this right now for structural reasons.
If you're worried about unknown markups, just shop at any one of the stores that says "Prices are same as in-store," and you're safe.
That being said, everyone at Instacart would agree with you -- secret markups suck, which is why we built this feature to tell you which stores are priced the same as in-store. The unknown markups don't exist because some guy in a smoky room twirling his mustache hatched a devious plot, it is just structural. The user interface should have reflected this reality earlier, and it didn't, but now it does. We really do want to be as transparent as possible with our prices.
If you have any specific feedback I can take it directly to the consumer products team, or you can email feedback@instacart.com. They love feedback, positive or negative :)