You could compile an actual syntax highlighter to WebAssembly and embed that into the font. That would address all the issues. However, WebAssembly is an off-by-default experimental feature for harfbuzz, so at least for now the current solution is the only feasible one if you want it to work in most places.
Another issue you'd run into, I suspect, is that in practice text engines/editors/etc will often repaint only fragments of the content, and so the syntax highlighter would not necessarily see all the context it needs.
E.g. if you have a comment that starts with "/*" and ends several lines later with "*/", but the editor decides to just redraw a line in the middle, the highlighter won't "know" to use the comment color as the text-drawing operation won't include the delimiters.
(This issue already exists in a small way, as mentioned in https://news.ycombinator.com/item?id=41251114, but it'd only get worse as the syntax highlighter becomes more sophisticated.)
