I am not a color specialist, but I thought that the XYZ components should never be negative. [...] In general XYZ values can be negative due to chromatic adaption (aka. color constancy). They do not automatically indicate some kind of "error". Clamping of such values should only occur for display purposes, not for intermediate computations or persistence (export/saving of intermediate state) and since XYZ is not a display space, this means it should practically never be clamped.