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I think a good way to do it is to embed the whole font, and select the embedded font at body level to make it the document default font (i.e. body {font-family: 'STIX'} ), and also select it for those special spans/paragraphs where you need the mathematical symbols.
This way if the reader chooses the "Document Default" font they see the whole book in the embedded font, but if they choose another font such as Georgia then they see the main text in Georgia but the special spans/paragraphs will still be in the embedded font.
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