Yes very specifically the Storage Unit swapping rules were actually changed for a short period during Beta 13 development to make sure that doesn't happen, but it actually lead to even more problems for players, so was switched back
I am somewhat curious as to what problems this lead to.
There won't be warnings added for this particular feature, you'll have to swap manually if you don't want automated behavior, which has very few rules and is quite consistent for the very reason that it's easy to predict what will happen if you let the automated system do its thing.
I do have to admit that i never actually use the auto-replacement feature to replace items from my inventory, in part because i didn't realize it existed, in part because those situations are rare compared to replacing equipped parts. As a result, swapping a part from the ground to replace an equipped item that then replaces an inventory item is something i almost never really expect.
Maybe i'm actually the only one it wouldn't bother to have the option to prevent the switching of both attached and inventory parts. If that's the case, then there is indeed not much of a reason to make that option!