A distinction must also be made between what Flash etc does, which is true 3d IC, and the Raspberry (and older smartphones iPhone 4 and 5 era)...
that is called package on Package, where a fully packaged ram chip is soldered onto a fully packaged processor. This is a completely different process, the dies are fully normal planar cmos ICs, the only difference with normal BGAs is that on the bottom IC’ PCB (i’m Talking about the pcb inside the package, not the motherboard) has pads on top that connect to the upper IC, as opposed to only on the bottom,and possibly a recessed cavity for the die.