This issue was resolved as Works As Intended. The reason is not that Mojang intends to create broken strongholds to annoy and frustrate you. It's because this is an unavoidable consequence of the algorithms used for realism in structure generation. There's a conflict between making generated structures realistic and minimizing the chance that they'll overlap (and therefore that one will be overwritten). Mojang carefully chose its generation algorithms to balance these goals, and that is where the "Intended" part enters the picture.
Unfortunately, it just isn't practical to ensure that overlaps never occur.