I live in HKG, most of my business travel is with Cathay, so what I say clearly doesn't align with the experience of others here, but I would say: QR is very sensible in making the "upgrade" offers more than the "standard" ticket offers as put bluntly they are targeting a market that may not have paid the base fare, i.e. corporate travellers who may be forced to fly in Y, but have to upgrade out of their own pocket if they wish to experience a better class of travel. When I do this I'm often paying ~20% more than if I bought the upgraded ticket directly on the website. Alas that is the cost of corporate compliance and the route to hotel and expense reimbursements!

By the way, and I may be wrong, but the reference to "two free changes" is not reflected into the detailed fare rules if I could find them easily: I seem to remember they are revalidations or something similar? So it seems like QR is entitled to charge whatever they do so wish to upgrade, as unless your fare rules explicitly say that upgrades are going to be free (not so typical on a cheap economy ticket rules), there should be no expectation of a cheaper/same price upgrade?