The stock fuel mixture is programmed on the lean side, in order to meet emissions requirements. In fact it is just on the verge of, but not quite so lean that the bike would surge or run so lean that it would be noticeable in normal riding.
The slip-on creates less back pressure. This means that the cylinders are more thoroughly scavenged. So instead of re-burning some of the mixture left over from the previous ignition, a greater portion of the mixture is freshly induced from the intake. The net effect is that it leans the mixture in the combustion chamber even more. Now the mixture has become so lean that it may misfire, surge, or simply lack power to the point of being noticeable.
If the mixture was programmed richer, the slip-on will produce more power. But to do this correctly, it may need more fuel at certain RPM and % throttle openings, and not in others. This makes the process quite involved, with the use of a dynomometer, etc.
I had developed an economy fuel program on my PC V, and a performance program. Upon switching the exhaust from stock, the bike would no longer run well with the economy program. I had surpassed the limit of lean mixture, and the bike ran poorly. I switched to the performance program and it runs great. You have to be gentle with the throttle, or the MPG will take a nosedive.