Yes the harness is hugely different.
The retrofit instructions show the retrofit loom and if you look at the circuit diagram, you can clearly see the methodology practised by BMW. IThe retrofit loom plugs into the existing vehicle loom with minimal work required; no access to speakers in doors needed at all.

In a car without nav, the radio is in the dash and drives the DSP amp in the trunk.
All antenna wiring, CD changer wiring and audio feeds go straight to the radio
Speakers are driven by DSP amp in boot, and the loom includes all speaker wiring to all speakers

In a car with nav, the radio is in the trunk, and the connection between DSP and radio occurs over a distance of approx 2 feet.
The wiring to the front of the car is just for the monitor.


In fitting a factory loom you must strip the entire car and remove all door panels and do much more work than using a retrofit loom

Honestly, there is no benefit to be gained with a factory loom!! You just create lots of extra work for yourself.