I think it's quite reasonable to want to offer upgrade pricing, especially to customers who recently purchased the old version. It's just good business to ensure your recent customers don't feel screwed over having to pay full price for the new version when they just paid full price for the previous version.

The issue here is the inflexibility of the App Store, coupled with the inability to handle payments and licensing separate from the App Store. While this tends not to be much of an issue on macOS (due to macOS allowing installing applications from sources other than the Mac App Store), it very much is on iOS as well as in cases like this (as Apple has restrictions on certain kinds of Safari Extensions being distributed outside of the Mac App Store).

As a customer who purchased the StopTheMadness Link Unshortener Bundle about one and a half years ago (and therefore missed out on the upgrade pricing, while other customers who purchased StopTheMadness years earlier received upgrade pricing), I do feel screwed over. Not by the app developer of course, but by Apple.