ExtremeTech spoke to AMD and got to hear that a Ryzen Threadripper CPU with just two dies under the huge IHS would result in issues. There have to be four dies under the hood to ensure there's no mechanical instability when coolers are mounted.
So AMD uses two real dies and two dummy dies to stabilize the packaging. The "fake dies" are blank silicon structural insets and they are mounted and soldered in the exact same way as the real dies. AMD does this to ensure they can use the same production line as they use for the EPYC CPUs.
Another interesting tidbit is that the two active Threadripper cores are placed diagonal from each other, to minimize hot spots:
They’re apparently structural inserts required for support, but do not represent “bad” Epyc cores or any kind of core recycling. OC3D also states that the two active die in Threadripper are on the diagonal from each other.
The die arrangement makes sense — using the two die with the most space between them ensures that hot spot formation will be minimized.