I usually set the correct "full throttle" boost, then adjust the engine to produce the correct power, and then use as much boost as it takes to produce the correct emergency power. I think my Merlin 63 and 66 are somewhere around +16½lbs when full emergency power is engaged while they should be at +18lbs but since I'm getting the correct power, so be it. The very noticable increase in charge temperature causes quite an efficiency loss but CFS3 doesn't know to handle that, it only understands losses as a function of rpm which remains the same. Back in the days of the Bf 109G/K series I used correct boost pressures for both full throttle and emergency power, as a result the engines were slightly down on power at full throttle. It's a matter of less than 50 bhp anyway so perhaps even falling into the production tolerances of wartime engines.
The throttle lever on the Spitfire had a "gate", probably some kind of a friction stop, to indicate the transition from "normal" boost to overboost. It wasn't all or nothing, if the pilot wanted for example +16lbs on an engine rated at +12/+18lbs it was possible, the throttle was simply pushed through the gate but not firewalled. There were actual restrictive devices to prevent the full travel (and thus full boost) from being used when engines modified for +25lbs were, for one reason or another, running on the normal 100/130 grade fuel instead of the 100/150 grade rocket stuff.