There are several things you can do to manage this for FM Go.
have a look at your layout...
... turn on Dynamic Guides to show the orange boundaries of the portrait and Landscape and the section which overlaps. This intersecting area is where you should layout your view for the iPad.
... make the header, body and footer sections fit in this area... including making the right edge of the layout area match the first orange line on the left.
You can also lock the zoom level to 100% in your open script.
I tryed the dynamic guides. That seamed to do the trick. Scripting is a little beyond me at the time, but I will be learning it soon.