So I have reviewed my video again, and I think that one may have some shenanigans at play there? Although they were two separate instances of rocks being broken, they were broken at the "same time". As in, I placed a bomb, and while waiting for the bomb to explode, I moved elsewhere and pickaxed a rock - at the same time the two actions execute and dropped a staircase and a hole.
The other instances of multiple staircases are more concretely from the same instance - as in one bomb unraveled multiple staircases/hole. I think that falls under your expected scenario though, and that still exists in 1.6 switch as of now.
Unfortunately, I don't think I've captured much of Skull Cavern videos otherwise because I wasn't actively screenshotting at the time for this purpose haha (... they are usually for more interesting phenomena like having 20+ bugs on a floor, or a huge cluster of iridiums at single-digit floors, etc.), but I just remembered my brother probably still have pre1.6 SDV on his switch since he stopped playing, if I can convince him to let me borrow his to play for a few hours I can probably test this more definitively (that is the hard part).
Other than that, now I hesitate to say I remembered properly except for the fact that there was a fundamental change to my "muscle memory" for the caverns. I won't be surprised if it was just that I was carrying large bombs and there just are more multi-staircases often as a consequence, or that the second sets of staircases are all from slain monsters after initially breaking open a rock.
That's all the update I have so far!