Thanks for writing.
The issue with the transparent system tray is a little trickier than normal. From the popup perspective it is difficult to determine how much to offset the popup content when a semi-opaque system tray is present.
Consider for example the case where the popup always takes into account the system tray regardless of its opacity and offsets the content accordingly. Now the fact that the system tray is semi-opaque makes no sense, there is no information to be seen under the system tray because everything has been moved out of the way.
Another case is where the user has modified the PopupItemTemplate to have some margin that is appropriate with any system tray configuration. In this case, if we offset the content, the items will have an even greater margin which is not what the user intended because the items were fine in the first place.
With that said, I suggest that you define two item templates with appropriate margins and switch them dynamically whenever your page changes orientation.
Please write again if you need assistance with anything else.
the Telerik team