The y-coordinates for the icons of autorotation, gyroscope and full screen are equal to zero.
The y-coordinates for the map, hotspot and information icons are equal to 109.
The y coordinates for the VR icon are minus (-) 92
The reason for the discrepancy is the fact that you have elements tucked away inside containers which are again in turn tucked away inside other containers. The X & Y positions of an element in a container are relative to that container. So if my container is set at X = 100px and Y = 100px and the element inside it has an X & Y of 10 & 10, and the element's anchor is top left, then the element will be offset from the top and top left of the container by 10px and sit at 110px x 110px in the skin.
In your skin the icons of autorotation, gyroscope and full screen are inside containers called, respectively, button_auto_rotate, gyro and button_fullscreen. The icons inside these containers have X & Y positions of 0:0 except button_image_fullscreen which is 1 & 0.
The three containers have the following X & Y positions. button_auto_rotate = -51px & -92px ; gyro = 29px & -92px ; button_fullscreen = -11px & -92px. The fact that all 3 have Y position of -92px means they are in aligned to their bottom edge.
Now all three containers are in another container called controller. Now the controller's X & Y is -118px & -119px.
The controller container is in another container called hide_controller_container and it's X & Y position is 1px & 23px and it's anchor is bottom center.
The map, hotspot and information icons are in the hide_controller_container so their X & Y positions are relative to only that container but their anchor point is set at top right.
The VR icon is in the hide_controller_container like map, hotspot an information but it's anchor point is bottom center.
In the image below I've highlighted all of the containers and pointed to their locations in your skin. This should give you an idea why they are all slightly out of place. (see image below)

- ipad-tutorial-1.jpg (301.31 KiB) Viewed 1506 times
I've gone through and repositioned all of the containers and elements so they are relative to each other as you move down through the container structure. (see image below)

- ipad-tutorial-7.jpg (411.23 KiB) Viewed 1506 times
I've also attached an updated skin file.
Tony