Removing the cat from the stock cat box leaves a large volume that the exhaust pulses see as an end to the system. This creates a place for the pulses to reverse, and alters when the pulses return to the exhaust valve.
Removing the box, and replacing with a pipe, allows the engine to have a longer collector length that better matches the needs of the engine.
This is similar to 3-2 exhaust systems compared to 3-1 systems. The 3-1 has a longer collector length, and the R3 engine tends to perform better at all engine speeds and loads as a result.
Just removing the left side pipe from a Jardine system can add a couple of hp throughout the power-band, simply because of the better tuned length of the system. This occurs even though the primary lengths of the Jardines are not what the engine wants for best output.
Increase compression, improve cam/valve events, etc., and this becomes even more important.
Something to think about.