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Hi Jongware,
The issue here is not document properties or cs5.
When you run your one line script you expect to see this 
note the smaller top margin.
BUTthis is what you get. 
all the margins are the same.
BUT as stated this has nothing to do with the fact one is trying to do this in the set of the document with using your one liner
app.documents.add({marginPreferences:{left:"0.5in", right:"0.5in", top:"24pt", bottom:"36pt"}})
or after the document is set up using my one liner
app.activeDocument.marginPreferences.properties=({left:"0.5in", right:"0.5in", top:"24pt", bottom:"36pt"})
or the multiline
app.activeDocument.marginPreferences.left = "0.5in";
app.activeDocument.marginPreferences.right = "0.5in";app.activeDocument.marginPreferences.top = "24pt";app.activeDocument.marginPreferences.bottom = "36pt";
They all will do the same and the screen will still look line screenshot 2.
BUT all these 3 methods HAVE set the document's margin preferences.
To see this you have to set the PAGE margin preferences.
after running the above lines do this.
app.activeDocument.pages[0].marginPreferences.top = app.activeDocument.marginPreferences.top;
Then you'll see that the document setting were indeed set.
To get the results you expected you needed to set the APPLICATION margin preferences.
app.marginPreferences.properties=({left:"0.5in", right:"0.5in", top:"24pt", bottom:"36pt"})
now when you do
app.documents.add({documentPreferences:{pageHeight:"10cm", pageWidth:"20cm"}});
You'll get the results shown in screen shot 1;
In summary as far as I see (which is not very far) using with properties is not at all problematic, one just has to be clear on the properties of WHAT one is trying to set.
I don't really see a lack in Adobe's documenting of this.
Hope that's crystal clear and to everybody out there DON'T FORGET TO RESET YOUR APPLICATION MARGIN PREFERENCES
Regards
Trevor
In a bit longer form than Larry put it.
I would guess the answer is that properties can all be set (except of id, index and that sort of read only stuff) but collection properties of collections cannot.
For example app.documents[0].rectangles
You can not set up a document and define the array of rectangles you want in it because to do that you would have to write app.documents.add({rectangles[0]:geometricBounds:[0,0,100,100]}})
The problem being the [0] this is because the key elements in the properties are keys which are strings and the string/key "rectangles[0]" is obviously not recognized.
Example 2 from Jongware
To make a pretty W in one line one uses (see http://forums.adobe.com/thread/1103517?tstart=0)
app.layoutWindows[0].activePage.ovals.add().paths[0].entirePath = [ [167,69],[147,123],[123,82],[100,125],[81,68],[72,72],[97,144],[123,98],[147,141],[176,73],[167,69] ];
For the above mentiond reason one cannot use
app.layoutWindows[0].activePage.ovals.add(paths[0]: {entirePath : [ [167,69],[147,123],[123,82],[100,125],[81,68],[72,72],[97,144],[123,98],[147,141],[176,73],[167,69] ]}});
So as a rule of thumb if its not a read only property like id, length or a collection property like rectangles then you can set it.
P.s. The above is all guess work but I think it's correct 
I have looked at the document object in the object model viewer and there are hundreds of properties.
Why on earth are you using the object model viewer and not Jongwares Object Model which is so much better?
Check out http://jongware.mit.edu/ for all the versions chm on windows is the best or http://jongware.mit.edu/idcs5js/
Trevor
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