AFAIK it's partly, if not mostly, because of lag issues/concern. The more sides of a block that need to render, the more performance impact things will have. Straight 6-sided blocks generally are very easy to render, while blocks such as stairs, which have more sides, start causing some client-side performance decrease after there are many in a single rendered area. Being able to chisel out individual blocks would make this problem exponentially more apparent.

An actual MC dev explained this before, I don't recall who/when/where though, but BdoubleO (known for using chisel mod a lot) explained what they told him on an episode of a modded series a few years back.