I agree, this seems like an oversight when integrating the new system into the old, as this wouldn’t have been an issue prior to this patch. I am getting pieces in LFR on alts and paranoia sets in when I go to upgrade an item, checking the dungeon journals to see what the normal ilvl is so I don’t upgrade to or past that point. I’m not even sure which alts I will run the higher difficulties on in the future (primarily doing my main in normal and heroic now), but it seems silly to be cut off like that when I am also capping flightstones and just want to upgrade them to 424.
At the same time, some people (including myself on various alts) may never run the content, or enough content, to allow them to upgrade past the actual “upgrade” point of the next tier. It just seems like the new system design while great in many ways, is a bit convoluted regarding the overlapping upgrade paths and currency needed (among some other issues).
It requires a bit too much forethought, planning, and RNG to make the most use of the system for everyone involved. “Will I run the heroic raid or proper mythic keystone level to upgrade past 424 on this alt? Not sure yet.” And the heroic piece is only a tiny bit higher ilvl on the top end. The idea of what constitutes an upgrade used to be a bit more straightforward, although there were issues with that system, too.
I also agree that putting in a suggestion in-game or somewhere else on the forum would be a good place to start.