Another oddball formatting question.
Going with the assumption that the first line of text isn't indented, when does that apply and when doesn't it?
As to the original question about indents, this isn't so much an answer as a bit of context. I think that what you're seeing with print books is basically a result of the publishing industry adopting styles from formal writing, but not having the constraint of having to adhere to a specific style.
The major point of the different styles has to do with citation: different disciplines put varying emphasis on authorship and quotation. However, because these styles are being taught academically, they also include all sorts of other details such as paper size, indent depth, spacing, font choice and size, and so on. This ensures not only that assignments are consistent but that students are practising the format they'll need in that field.
There are several major styles used in academia, the most important being:
APA (American Psychological Association) is used in the social sciences. It has two indent styles: first line indentation and hanging indentation. Most paragraphs have the first line start 0.5" to the right of the other lines (first line indent), but reference lists use a hanging indent where the first line starts to the left of the rest of the paragraph (like a bullet-point list).
Harvard style is very similar to APA, but is used more in the UK and Australia, especially in the humanities. Notably, Harvard recommends getting into the habit of indenting paragraphs as you write, the other formats assume that you'll put indents in later as part of the formatting process.
MLA (Modern Language Association) style is the format most commonly used in the liberal arts and humanities, especially in the USA. In MLA, the first paragraph of a chapter or section has no indent, and all following paragraphs are indented. This is the format that I'm most used to using (West coast Canada, English dept.).
CMS (Chicago Manual of Style) is uncommon at the undergraduate level, but sometimes used in the humanities; it is mostly used for history and economics. CMS recommends that all paragraphs be indented using the TAB key. This is a growing issue since some ebook formats don't recognise TAB as a standard indent format.
The other two major styles in use are Vancouver, used in medical and science papers, and Turabian, which is a version of CMS adapted for students rather than being focused on publishing.
So if you are really worried about consistency, you might actually want to pick up a style guide and stick to it. Failing that, I'd say to just go with whatever makes you comfortable and don't stress it. Most people really won't notice.
Personally, I mostly use MLA when writing. I'm used to it, and I'd rather use a formal style when writing casually than have to break myself of bad habits later if I go back to school.