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The ncxgenerator.py generates your second example (which is what creates it from the Nav). Any time it is changed after initial creation the NCXWriter code which uses Qt QXmlStreamWriter with auto formatting set to true and default indent of 4 not 2. I can change ncxgenerator.py to match the indented head tag and change the QXmlStreamWriter to use indents of 2.
I'll try to get that into the next release when I get back home.
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