Other than cost versus price points; another reason manufacturers do not perform many of these mods themselves, is the simple fact that many of those high grade parts are not available in large enough quantities to make enough units, or the supply is unreliable. I can remember a conversation with Stan Warren, where he commented he was backed up because he was having trouble getting some Black Gate caps. If Stan can't get a couple dozen quickly, imagine Sony's problem.
Also in many cases it may take too long to manufacture the unit in that way, so labor cost would be too high.
If you want a YBA made in France, you have to pay up; or settle for the cheaper Audio Refinement made in China. Same for the Creek designed gear for Cambridge Audio.