The thing is, this is the kind of build that Transcendence pushes for. Pushing out as much CDR as possible with the most efficient items is exactly what was designed for it to do. However, there aren't enough 20% CDR sources that aren't UNIQUE to support it, so stacking the same item multiple times is the only way to most efficiently make use of the rune besides maybe adding in a Trinity Force into the Black Cleaver stacking.
In short, this isn't something cheesy that slipped through design. It's how the rune wants to be used, it just doesn't have enough diverse support for it not to look cheesy. If Morellonomicon and maybe Nashor's Tooth didn't have UNIQUE CDR, the same would be true for AP champions. We might see people stacking multiple Morellonomicons for maximum mana, ability power, and CDR.