Removing the cat in some of the earlier bikes featuring them (e.g. 2012 Victory's fitted with the 106 Freedom motor - where they were literally squeezed into same-size headers) would affect engine performance, most notably the amount of valve overlap due to the altered back-pressure and how that bears on scavenging exhaust gas. Most modern bikes now sport larger cats, specifically not to impede gas flow and mainly to deter motorbike/car owners from removing them.
Adaptation affects the entire rev-range. The latest ECUs continuously adapt to manifold airflow and pressure sensor readings (amongst others increasingly) in combination with what the O2 sensor(s) feed back, to maintain a chosen stoichiometric A/F ratio (e.g. 14.5) - to an extent even considering one's riding style. By resetting it after installing new slip-ons, the ECU will clear current adaptation values (throughout the rev-range) and readapt afresh - normally over at least 300 km. In the case of the KTM 1190/1290 ECU, with which I am more familiar, it will even readapt correctly when fitting a different air filter - no need to get a dyno-tune for that on those KTMs.
Loading a map, like Penner's, does other things. Like altering throttle-body behaviour, enriching the A/F ratio in specific rev/throttle load regions and adjusting other engine response parameters - specifically to improve performance and rideability, and move away from overly lean settings imposed on manufacturers. Performing a dyno-tune, in place or in addition to loading such a map, brings it all to even a higher and more individualized state-of-tune.