You can increase the IPC by adding more transistors as the silicon shrinks, but that isn't what the 40% improvement figure is based around. The 40% number is solely design improvements independent of the process. If Zen was a 28nm CPU like the Carrizo, it would have a 40% IPC improvement.
The Excavator alone is getting a 4-15% IPC improvement over Steamroller without any reduction.
Well that's the whole thing, without the process you won't get the 40% IPC, as chips get more complex to design and as reduction in nodes (process) doesn't give as much benefit from power consumption and performance through frequency because of leakage, design has more influence than process to get where you want to be, but process is still part of that because design restrictions are applied by the process.
When you have per clock improvement of 40%, what will the clock speed be for a 14nm Zen, it might not be much more than current CPU's, and that will still stick to that 40% overall increase, hopefully that is not the case they might be able to get more frequency through better design but that is all up in the air. Intel hasn't really been able to increase frequency much of their CPU's even though they have much more control over the process and libraries they use.