The reason I took away from this: large agricultural producers of peppers bred towards a "low heat, low variance" standard, away from a "high variance" standard that produced frequent hot jalapenos. Low-heat-low-variance is better for mass food production, because producers can just dose the capsaicin directly, which is something they can't do easily when every pepper is a wildcard. There are second-order effects, li…
Less spicy is actually good. I prefer more flavorful chiles, with less spice. Mark Miller's conversation with Tyler Cowen is good on this subject: https://conversationswithtyler.com/episodes/mark-miller/ . Chiles are actually fruits and, combined judiciously, create a lot of complex flavors. Excess spiciness overwhelms the flavor. And people who want absurdly spicy peppers, can get them: ghost chiles, carolina reaper…
Two problems with this idea as applies to the article. First, it's hard to separate the two in breeding (many of the most flavorful chiles, far more so than jalepenos, are pretty hot).
Second, industrial production optimizing for a lot of things: shipability, stability, shelf life, consistent size/appearance, in this case consistent capsicum ... most of these are considered more important than flavor according to revealed preference. Consider the current "standard tomato”. Round, dense, deep red, mostly flavorless.
So unfortunately you're likely to end up with a jalapeno that is more consistent, less hot, but also less flavorful - but looks good in the grocery.