There are already [Random] warp combos. So how about [Random Only Once] warp combos (or perhaps a Screen Flag by the same name)? Either would function the same as a [Random] Warp but would only be random the first time. Afterwards it would continue to use the warp that it originally picked the first time.
Using this, you could do a number of cool things, such as have four variations of a dungeon and only be able to play through one of the variations. (Kind of like Four Swords in LTTP for the GBA)