My guess is that lots of guys pick the MPI super over a turbo because the application is different. Supers are beter suited for corner to corner trail riding etc where power at the bottom end is desired where a turbo likes to be taped to the bars and provides it's boost at the top end. By installing a head shim you would lose the bottom end snap that the stock compression provides which would work aginst the point of having a super in the first place. I would think this is why MPI does not recommend the shim, To my way of thinking there is no reason you could not run a headshim on the super other than for the reasons above. It should work fine if you are pinned all the time but for sure it would not have the same throttle response.
All of the low boost kits are set in the range of 8,9,10 lbs max depending on elevation when running pump premium, if you go above that boost you need the octane. The Nytro motor enters the danger zone at around 10 lbs on stock compression without race gas. Your only 2 choices short of a complete engine management system are to lower the compression or raise the octane. The intercooler helps but even with that you will blow up the motor on pump.
One other thing to consider is the MPI turbo kit I saw last year at the show was built with a Mitsu 15G turbo which is a pretty basic turbo. A 15G is smaller and spools slower than a 16T due to the older turbine design so with a shim it would be even worse. When you compare the compressor maps the peaks are quite close but the 15G is old school so it benefits from stock compression. You will be pretty much off the map at 12 lbs with that turbo, it'll make more boost it just won't make any more power.
M5