Honda is not the only brand to have imperfect factory jetting.
The 2 stroke KTMs in the 90's and 2000's were jetted very rich down low resulting in black spooge running out the muffler. A whole generation of riders went through running expensive oils in smaller and smaller amounts in their fuel.
This actually made the problem worse as it was excees fuel the was causing this mess.
It was the first part of the needle that caused the problem and a change away from factory needle profiles resulted in crisp performance and a clean back end.
There was still sufficient fuel so running lean wasn't a problem.
I think the factory needles were this way as a simple fix for traction control.
This was before Map switches were even thought of.
Big bores often have similar jetting to the standard bore engines simple because they suck the air in harder resulting in more fuel being sucked through the jet.