IIRC The chip used for the Raspberry PI was built using a similar idea. It doesn't sound as advanced but generally similar. Broadcom mounted the dies for the GPU and RAM on top of the CPU in the same SoC package.
This is POP packaging. Part on Part. It takes two normal chips, fully encased as usual, and stacks them, usually using something like BGA. They are different dies, built at different times, and probably in different fabs, then assembled later.
3D chips are different. A typical flat chip is made up of dozens of layers of depositation and etching. You start with a bare wafer, and etch part of it away, then deposit a thin layer on top of that, then etch part of that away, then deposit another layer, and etch, etc, etc. You end up with a flat 2D structure of 3D objects, made all at once.
A real 3D chip has layers of groups of layers, creating a 3D structure of 3D objects.
Right now, we have problems moving heat out of the chips we have, and not so much problems with a lack of transistors available on a die. But that's how progress works, the best we can do is the product of a whole pile of limitations, and people are busy fighting back all of them. In time, 3D chips will become just "chips", just like color TVs all became just "TVs".
