Differentiated? As opposed to surreptitiously mixing business class seats randomly among the Y sections? All airlines "protect" their premium product by having armed guards stand around the J lavatories. Sorry, I mean by pricing it higher than Y, making it accessible to those who can afford it and protecting it from poor folk.

In all seriousness, QR has the data. They expect to sell a number of J seats for a given route on a given date. If they expect to have some empty seats, they often attempt to monetize them, just like everybody else. The goal is to maximise this revenue. Some airlines do auctions. I remember some 10 years ago being able to UG on KL when during boarding (FAs had tablets and you could use cash or FB miles). To each his own. Some airlines say they "protect" (I threw up a little in my mouth as I typed that) the J product by making UGs expensive. "Protect" is corporate speak, of course; they don't want flyers to catch on and buy Y fares and upgrade cheaply later. Nothing and nobody is being protected; the "if you want J then buy J" is a marketing game that is decades old. It's all about the marketing strategy. Airlines have some data to support this, but more importantly some people make the decision / prediction and ultimately that's that.

QR is in full control of how they sell UGs. You make a good point about 2 individually priced segments VS reticketing the entire itinerary... but ultimately QR is in control of their pricing. If someone high up decided "charge EXACTLY <x> amount for upgrades" then that's what would happen. IT systems enforce decisions that people make, not the other way around.