The document was created in Adobe InDesign CS2 (4.0.5). This means all the features you find unappealing are the result of conscious decisions. The strange use of empty pages is due to being a print on paper document governed by the strict rules of an academic thesis.

I also think the designer is working in a different tradition to the one you value. I see echoes of the work of Donald Tufte, Jost Hochull and Hans Hagen.