Adding a 'tuned' exhaust is essentially increasing the engine's Volumetric efficiency, on the exhaust side. Every advantage has a disadvantage. Making Efficiency gains in one area without considering other areas may or may not see increased performance realized at desired or key locations on the power curve. Even overall performance can deteriorate. Carb venturi size, intake port design, valve head diameter and stem design, cam profile, ignition timing and gear ratios should be considered. All systems acting in concert with one another provide results. Increasing Thermal Efficiency is a challenge. Only about 20% of the gasoline in your tank is actually used to produce work to convert chemical energy into thermal energy and onto mechanical motion,to end up as power (work) and torque. The hotter the engine operates, the more efficient it is, to a point that is. Mechanical Efficiency can be increased by reducing friction within the engine and drive line. A new engine has poor mechanical efficiency at first due to high friction from the cylinder wall crosshatch honing. You will notice that as the engine 'breaks in', power and torque levels increase and stabilize. Certain oils and lubes reduce friction more than others.
When an engine comes out of the factory, it is engineered for reliability, reasonable power and low emissions. The engineers took the time to 'balance' (match) the parts. Example: designing all the parts to work well together, in efficiency terms. Think of it like this: you decide to remove the stock muffler to install a 'performance' exhaust system. You may or may not realize performance gains. Think of the engine as a pump. If you make the outlet channel bigger, will it make the inlet side automatically flow more too? Think about it. Most carbs can handle the modest increased CFM but the fuel jetting would have to be addressed to enrich the air/fuel ratio accordingly. More air requires more fuel to maintain the proper AF ratio to around 14.7:1.
There are many cool tricks you can do to squeeze more power from an engine. I bumped up the compression ration on a two stroke and bolted it down to a workbench. I ran alcohol and caster oil in it with opened up jets. That puppy SCREAMED! Balancing an engine's rotating assembly like the flywheel, crankshaft, clutch hub assy, etc. really works!! Getting the air that enters a carb to enter straight (as in a stream of air) will also help. On 4 strokes with adjustable valves, tinkering with valve clearances can add a little performance at certain RPM's. Keeping the valve heads clean and carbon deposit free ensures continued performance.
Most of the stuff i played with over the years have been big engine muscle cars. the same can be applied to bikes too! Vibration and un-balance are power working against you! Something out of balance by 1/4 ounce can turn into nearly a hundred pounds of imbalance at high RPMs.