A book-quality PDF isn’t just “big text with margins.” It’s a consistent relationship between elements: which text is the primary heading, which is secondary, which is a sidebar, and which is body. Templates depend on those distinctions. If your source has headings embedded mid-paragraph or inconsistent line breaks, the template cannot reliably apply the right spacing, and you’ll see problems like headings colliding with the footer/header area or extra whitespace where there should be tight transitions.
Use a simple structure test: export or preview a page that contains (1) a chapter opening line, (2) a middle-of-chapter heading, and (3) the densest paragraph you have (often where you also have quotes, lists, or a short table). If each element lands cleanly without awkward breaks, you’ve aligned hierarchy successfully. If not, adjust the hierarchy in the manuscript rather than trying to “fix” the symptoms after export, because page furniture (running headers, page numbers, and chapter-start spacing) will continue to place those elements according to template rules.