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Browsers are sometimes helpful and try to interpret what you mean, if you don't want a page to be indexed, or want a different URL as canonical, you probably don't want search engines to guess. (SEO is to a large part about not making search engines guess.)
In short, avoid making the <head> brittle if you care about those SEO settings, consider moving them to the top of the <head> (don't include 5k lines of JS above them), and double-check the rendered DOM in your browser from time to time.