It does let you repeat them over and over. You don’t have to change difficulties in-between, and the mini-boss is just another explore battle with one harder troop.
Think of it like the old explore when mythics you owned could randomly show up, or when you got unlucky in Shentang and had to fight Yao Guai because he was part of the quest progression.
EDIT: I suppose I do agree that confirming the difficulty all the time is annoying. Less annoying than changing it, but needless as the pop-ups for the two boss battles.
Sorry—seems I misunderstood the complaint!