Hi Garp,
I don't know the answer to your question but in my years of experience, I have never had any 'fruit' rot on the plant.
I have grown many varieties, including having to fashion a humidity tent (using a LOT of cling film) to grow jalapenos in the house as I don't have a greenhouse. I have grown some that remain Green and some that ripen to Red and others that change to all sorts of colour from Yellow through to Purple. The ones that ripen to red, I sometimes harvested a few early whilst still green so they wouldn't be so hot.
The ones that ripen have always changed colour from a tip upwards or as a light bulb slowly being turned up (Cherry Bombs). The only thing I ever experienced was the flesh becoming wrinkly when they had begun to over ripen.
I hope that helps though I suspect not, sorry.
BAJ