Any motorcycle manufacturer can try to save money on suspensions or on the quality of the paint, for example. But it will not do it in the exhaust pipe, it's a cheap and very important part.
No one better than the manufacturer knows the type of exhaust that the engine needs. If you like to make noise, go ahead, but the behavior of the engine will not improve.
You can pay 1000 USD for a Termigioni, which has a manufacturing cost of 50. It's up to you.
This statement is not entirely true.
The manufacture certainly does know what the engine best needs, but that has to be tempered with local and international regulations which are quite typically far from ideal performance parameters. One of the factors brought on in the past decade or so is the requirement for catalytic converters which need to be integrated into the exhaust system and a key reason why we see "bread box" type features in many exhaust systems.
If you replace the items causing restriction (both exhaust and intake in balance) you can certainly make more power, closer to what the engineers had in mind when designing the engine and often near what you see on racing bikes.
Systems such as the factory sponsored Termis etc. are sold as "race only" in most cases and do not adhere to the full regulations and often are supplied with a corrected ECU map to compensate for the changes in airflow. Usually that high Termi price includes a new ECU map which on the open market typically runs around $450-500 to have a ECU reflashed so take that into consideration when comparing the price.
If you make the statement that you probably can't beat the performance of a factory system while still remaining 100% legal in all markets the bike is sold in, you are probably correct. Sometimes you can do a little better on the tone or lose some weight which can also be a reasonable motive for change. In the case of the Sled, I removed 10 lbs of weight by replacing the OEM CAT/muffler (13 lbs) with a Leo Vince GP style slip-on (3 lbs).