The Keihin ECU is not nearly as smart, nor as fast, as many modern automotive PCMs.
It uses a narrow band Lambda sensor to target Lambda 1.0 at
idle and cruise.
At wider throttle openings than 6-8% TPS, it cannot keep up and is out of its narrow operating range. It will not correct for even richer requirements at even 20% TPS.
It can slightly increase overall fueling if it sees excessively lean conditions at idle and cruise, but only by very small amounts.
As a result, is cannot correct for larger increases in intake and exhaust flow through the engine.
Think of it this way, if you decrease restrictions in the exhaust or intake, more air is entering the combustion chamber due to improvements in flow and pulse tuning.
More air demands more fuel for correct operation. Stock maps are designed for emissions and noise reduction. They can be seriously lean in stock form. The further you modify the engine from stock, the less the stock mapping will be correct for your needs.
A simple change to a less restrictive silencer, with or without catalyst, and altering the secondary operation, is more then the ECU can handle on its own.
With the release of FREE software that uses an inexpensive cable (less than a few gallons of fuel) for interfacing with the ECU, and many working on freely (soon to be) available maps, the excuse for not giving the engine what is wants and needs, just doesn't exist anymore. Even just downloading a canned map can be a big improvement.
It is not like you are riding a Jap cruiser and your only option is to purchase a piggy-back fuel controller. For the price of that controller alone, you can now pay to have your bike fully and correctly mapped.
I hope this helps.