Best Camera Orientation for optimal quality and efficiency

Hi,
I have a Nex7 camera ready to be mounted on a Skywalker for an aerial photomapping operation. I am debating on whether to mount the camera with the base parallel to the wings , or with the base parallel to the fuse. Here are the pros and cons i have noted so far :

Base parallel to the wings :
Pros : WIll reduce the number of parallel strips, so will increase the efficiency/reduce number of flights needed.
Cons: Camera cannot fit completely inside the fuse and will protrude out.

Base parallel to the fuse :
Pros : Fits neatly inside the fuse and easier to mount.
Cons: With the camera sensor at 4:3 we will need to increase the number of parallel strips flown and thereby increase number of flights and also increase the time it takes to cover the same area.

Also came across this page : http://www.adamtech.com.au/Blog/?p=245

But couldnt understand how the height accuracy increases in the second case ?

Would greatly appreciate help in taking this decision !

Thanks

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