Hmm... Well, it seems Retina is a somewhat confusing term where the most important criterion is pixel density, or how many pixels per inch a given screen has, rather than the overall resolution. For example, the iPhone 4, the first Retina display, had a resolution of only 960 x 640. And on my old 4S (has the same resolution as the 4), Machinarium doesn’t display full screen—there are little horizontal bars running the length of both the top and bottom of the screen:
It's similar on my iPhone 7 Plus, but the bars are on the sides:
And I also have an iPad 6...the display size is 9.7”, and Machinarium has those black bars on the top and bottom of the screen:
So my assumption is that you’re referring to a similar issue, and perhaps those black bars on the top and bottom are even thicker when playing on a 12.9-inch iPad Pro, and maybe even with black bars on the sides as well. If so, I believe that's just a limitation of the game itself; even the PC version of the game looked like that when the game was released initially, as the maximum resolution was 1250 x 790. The developer explains this in more detail in this post:
http://forum.amanita-design.net/index.php?topic=175.msg610#msg610
