Production car components are designed and built to a tight budget, as well as having to comply with worldwide (in most cases) noise and emissions regulations. They are designed to make the engine as flexible and driveable as possible, not to produce absolute peak power regardless of the consequences. Aftermarket exhausts are not governed by these restrictions and can be of higher quality materials, made with more care, and optimised for performance with fewer compromises.
Some aftermarket exhausts are optimised for peak power at high revs and are large bore with minimal restriction to flow. Great if you want peak power at 6000rpm or more but they can compromise torque at lower revs, where a smaller bore system (or at least downpipe) can be preferable. This may be the difference that Marlon noticed - probably better low and mid-range power with the standard system with a slight trade-off at high revs which probably wouldn't be very noticeable.
The same bore considerations apply to carburettors - fit twin Webber 40DCOE's/IDF's to a 2 litre engine and the flow rate through the carbs will be at its best at low to mid revs, with peak power slightly restricted. Fit 45's or 48's and low-mid range is compromised (in this case, air flow speed is too slow for optimum atomisation of fuel) but at high speed the increased bore size will allow higher peak power.
As with most things in life, car engines and their ancilliaries are a design compromise - the manufacturers find what they consider to be the best compromise and then we choose a different compromise when we modify what they designed.