1. What I mean by working on the content of the book is more about how many pages per section, getting an overview of the whole. My client in this case is an institution with a collection of very rare books, I'll have a look if I find Lilliputians behind the shelves. The page size I'm printing my thumbnails on is A3. The thumb size is big enough to read a section name and page number.

2. Being able to apply colours to the Masters is something I've asked Quark for years and recently suggested in an InDesign wishlist to Adobe. I'm still amazed that this function wasn't part of a previous version. When you work on a 200 pages documents, it has to be visual to help you get an easy view of the structure of your document. To me the Print thumbnails option is in the same category, so I was expecting the labels to be displayed.
As for scripting, I've done a bit in Python when working on typefaces in FontLab Studio but I'm not familiar with InDesign scripting at all, unfortunately. I should have a look and thanks for pointing out this option.