So why does the A-380 work and this doesn't?
Because the A-380 is a clean-sheet aircraft designed to carry ~500 people from the onset while this is stick-on kludge-engineering onto an airframe that can't possibly do the job.
Note that all of the stretching of the 747 frame from the -100 on has for the most part been fore and aft the wing spar, including (actually,
especially the upper deck. You're stretching that deck to encompass the whole length - that's spoiling aerodynamics, that's adding a lot of structural weight in places not stressed for it (I'd be willing to bet it'd quickly break its back) and adding a lot of complicated engineering onto a frame the designers had never, ever intended it for. Even if you stress the pressure hull to take that, for example, you've just added a bunch of weight that now makes it questionable if the aircraft can even get off the ground. And the cross-section of that upper deck is very small, about that of a 737 or less, while the A380's the equivalent of two jumbos stacked on top of each other - so you're still not going to match the capacity of an A380 and it's questionable if the extra load would justify such massive changes.
It's relatively easy to add frames in between something, but this is far more complicated.
It's not physical engineering issues
Well, in this case, it is.