Ignore the engine power figures, the only meaningful power a wheel dyno can give you is the one at the wheels, anything else is just a guess to try and give the customer a number. The only way to get a flywheel hp figure is to use an engine dyno.
50hp loss sounds way too high, I'd say 30-35hp would be a more reasonable estimate for a standard(ish) altezza. Also, the biggest portion of the drivetrain losses come from the tyres, which is a major variable, even in back to back runs, unless you monitor their pressures and temps and keep any strapping the same.
A hub dyno would get you closer to a more accurate flywheel figure as it eliminates the variable of the tyres from the measurement.