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Flywheel HP is the total HP that the motor is making. Rear wheel HP is the power that the car is putting to the ground after drive train losses, IE: mechanical inefficency and friction losses. Rear wheel HP is better, an actual indicator of the car's performance, and what is measured on a dynomometer. A typical vehicle will lose + or - 15% from the motor to the rear wheels. Auto trannys are worse. :D
As said, the engine produces the power. The drivetrain consumes some of this power leaving somewhat less available at the wheels to actually move the car. So the critical amount is how much will actually be available... and that is RWHP/RWTQ.
Also as stated a manual transmission drivetrain is more efficient than an automatic and therefore passes more of the engines power to the wheels. Around 15% is lost with a manual and around 20% with an automatic. These are not exact number but close enough.
So, if your engine makes 400hp at the transmission... with an manual tranny you would measure around 340rwhp. With an automatic you would measure around 320rwhp.