Why is it an issue even with clipping? [...]
Not a big issue. Such inaccuracies are rare, but when they do pop-up, the inaccuracy isn't a problem. The same happens with Cbox calculation in traditional glyphs and we are fine with it too. :) The glyph will still land up at the right place.
[...] The clipped bounding box can be
very well estimated as an overlap of (1) clipping path bbox and (2)
drawing path bbox. This should be good enough.
I guess that's an internal detail of bounding box calculation and we are not dealing with that. The library authors or the authors of the graphic backends should deal with this. We just use whatever they provide.