I would expect modern icon fonts to exclusively use the Unicode Private Use Area. Fallback fonts would then not have glyphs for these code points. Screen readers would hopefully ignore them.
Screen readers ignoring them is a problem when it is UI the user needs to interact with. How does the use know that U+E9AF is the Edit icon they are looking for versus say maybe U+E9AE is the Delete icon?
They don't. That's is why icon-only items (links, buttons, …) must always be explicitly annotated, using aria- attributes. You can do this with any icon technology. You wouldn't annotate the icon itself.
