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In a general sense, PDF *as a format* is fine with embedded variable fonts. As ever, you (should) end up with a static instance-font in the PDF. But that does not mean that every workflow is OK, or that a given workflow is ok with all fonts.
HOW exactly is the user is generating the PDF from PowerPoint? On what platform (Windows, and if so, version?). File>Export using presumably Microsoft’s PDF generation? Or something that patches the printer driver?