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A "profile" is a collection of settings for the various command line options, one of which is the layout-mode. When you choose "Default" layout in the GUI, you are using the layout defined in the profile.
I have set it up to always use the reader's portrait mode: the reader's landscape mode is never used. If you choose to switch to that, it will not look good as the resolution targeted is for the portrait version. So avoid the reader's landscape mode in general.
As you correctly found, the prs500 profile is for portrait and prs500-l for landscape (holding the reader sideways). There is always some amount of overlap between pages in landscape mode (20 is default), so I'm surprised that you got no overlap. Can you just try using the default settings, just changing the profile to prs500-l and seeing the output?
There is also a major difference between landscape and landscape-half layout: landscape will take as many pages as necessary to show the page in correct aspect ratio (it may be anything from 2-4 pages) while landscape-half will resize the image to fit two pages then chop it up.
I've been meaning to release 1.8 for a long time now, but am travelling at the moment so no chance... probably will be resume development from next weekend onwards :-)
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