Have you actually tried exactly what you described? For epub and kepubs, making an annotation works exactly like that. And a long-press and drag to highlight multiple words. For other formats, you can tap the top-right corner to make a bookmark and then add a note to that later.
You can view the annotations from the annotations list inside the book, or from the books menu in the book list.
There are various ways to get the annotations out depending on how you want to use them. There is an option you can add to the config file to have an export from the books menu.
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