Nathan,
You almost have to reference the control side of the pressure control valve to manifold pressure in a turbo set up or it will be almost impossible to get the correct tune. The injector is an orifice and the flow through an orifice is proportional to the square root of the pressure differential, so if your fuel pressure is at 40 psi and your manifold pressure goes to 15 psi then the differential pressure will be 25 psi and the fuel flow through the injector will be reduce by about 20% and you will find that aluminum form the top of the piston is a pretty poor fuel. You certainly could set your fuel curve to compensate for this but it would only be accurate at one differential pressure. On my little 2 liter Zetec engine in my modified I reference the control pressure to the intake manifold, it is normally aspirated, and it made a big difference in the mid range drive ability,something you probably not concerned with.
Another thought is running a smaller injector at a higher pressure (dieselgek please comment here as I am sure you have probable done this) which should give you better resolution on your tune up. If you ran at 60 psi you could then run an injector that would be 22% smaller and get the same flow. I am not sure what the maximum pressure that the Bosch style pump will run at but I have ran my Bosch pump at 75 psi before and did not have a problem.
Regarding your use of a second pressure regulator as a dampener, as you said the part that does the dampening is the diaphragm in the valve, using a piece of -6 hose with a plug in the end and tee ed into the very end of the fuel rail would do the exact same thing and be cheaper and probably do a better job. That is a trick from my old hydraulic engineering days,we used this as a fix for a control problem on a 5000 psi pump, worked every time.
Rex