I have experienced that naturally grown fruits have longer shelf life and observed the below:
Their skins are thin, thereby allowing the fruit inside to ripen quicker relative to fruits that have thicker skins
Their skin to fruit space is less, almost no air in between. I have seen it in natural Banana, Mango. It takes more effort to peel off the skin compared to unnaturally grown/unnaturally ripened fruits. It appears this reduces micro organism growth and attack within fruit.
They ripe quickly. Though outer skin seems still semi-green/semi-yellow, inner fruit is almost ready to eat - you can tell it by touching it and actually eating the inner fruit. I have experienced it in Mango. My take is most fruit liking pests get defeated by this nature of natural produce thereby increasing its keeping quality
The fruits yield early. This season, when I was yet to see rasapuri mangoes in market, my rasapuri variety tree was already yielding delicious fruits
I am no expert to accurately determine chemically/botanically the cause for better shelf life, please validate my experience with yours.