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Marvin never modifies HTML in ebooks - However, it "flattens" the annotations into HTML (in memory) once an EPUB section is loaded so, say, page flipping performance and reading performance shouldn't be affected. The only place where I can see degradation is when opening a section containing many hundreds of highlights but Marvin is heavily optimised to deal with this too.
You could try the free version of Marvin with a couple of books of your choice, create a bunch of highlights and see how it does.
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