I think they were implemented so that if someone wants to simulate a "minimal unlocks" gameplay, he can do it on a regular profile. Just like god preps were done to prevent the need for scumming.
I generaly don't have much use for them - I'm not even all that happy about keeping the spoon in there. Not having niche stuff in the shop pool prevents you from finding cool interactions and just about any item can come handy at some point.
If they were more easily available (I'm currently grinding my fifth after havign done all the gold challenges), you could "weaponize" an item tier - veto enough basic/quest/elite stuff to limit the ammount of stuff that can show up. Unfortunately this also limits your options, but if you want "optimal" or rather "cheezy" runs, or just try out a particular strategy dependably (in, say, VICIOUS Gaan'Telet) theyre nice to have.
I used to keep Spoon, +10 HP pendant, +2 Mana Pendant and the balanced dagger in there. I took the mana pendandant out and put Hero's Helm in there, since the helm costs a bit too much for my taste, and I've taken the dagger out for testing and stuck a rock heart in there which I'm not too hapy about and might replace it with the Battlemage Ring, which is good but possibly overpriced ATM.
I almost got pwned by Shifty Brickwork!