So I was holding my fingers crossed all this time and hoped it'll get fixed with 2015.0.1 update. Nope. Still exists.
The problem in a nutshell: I need to copy a folder or a single layer from one doc to another. Into a specific place within the layer list. So I stack two document windows side by side, mark the place I'm interested in in the receiving doc by clicking on the folder/layer in the layer panel. I'm now dragging my stuff from the donor doc and hoping that it will end up in that very specific place within the layer panel of the receiving doc. But Photoshop just places it in the very top of the list. Every time. Same way it did with the duplicate layer which is now fixed. Same way it still does with the smart objects dragged from the Creative Cloud panel. Errgh.
OS X Yosemite, 2 extensions that never affected anything, PS v2015.0.1