I think it's likely that the lower restriction in the exhaust caused a leaner mixture, which then heats up the exhaust pipe more.
Since there's no O2 sensor on your bike,the ECU has no idea that anything has changed.
However, you might be ble to "fool it" into richening up the mixture, by re-positioning your Throttle Position Sensor, to make the ECU think you have the throttle open more than you do, and thus have it squirt more gas in at the smaller throttle openings.
That would have to be a "trial and error" experiment, to see how much you need to move the TPS to "recalibrate it" for your needs.
But, I think it would work.