Mostly just a (fully justified) hesitancy to change JMB's design, I think.
Maybe. Sometimes there are valid reasons for leaving (some) things alone. Remember what the gun was originally intended for.
Lowered ejection ports are most often done to prevent dinging up brass. Reloaders don't like ugly ammo, and I understand that. Dinged brass sometimes causes problems...but lowering the port also provides a bigger opening for debris to enter the works...which can get you killed when the gun is carried in adverse conditions. The gun was originally intended for a soldier to carry to war. Nobody was concerned with the condition of the brass after it left the port. The only concern was that it get out of the way.
Ski ramp rear sights are nice. They provide a finished, custom look, and provide a good sight picture...but they also negate the ability to operate the slide with one hand by snagging the sight on your belt or into the fabric of your pants. If you're in a fight for your life, with one hand or arm disabled, that can be important.
Upswept safeties are also good for preventing blistered hands, but they cost the shooter a solid, repeatable spot weld.
Ambi safeties do have their place, but they often fail at critical moments...especially if not properly installed.
Big, blocky sights are also nice for target work...but they do almost nothing to enhance shooting in extremely close range emergencies, where the gun is most likely going to be used...and they can snag on clothing and foul up the presentation...which can get you killed. When I carry a revolver concealed for purposes of self defense, I never carry one with adjustable sights for that very reason.
Most of these modifications came about as a result of game playing, and shooting prodigious volumes of ammunition...which is a good thing...but they also cause the gun to lose something of its utility as a fighting tool in the process. Like a crime scene...Everybody who breaches the tape brings something in with them, and when they leave, they take something out with them. No such thing as a free lunch.
So, the usefulness of a modification depends partly on what the gun is intended for, and under what conditions it will be carried. The right tool for the job.