Yes, a decompiled NCS will never exactly match the original source. That's impossible. The more extensive and complex the code, the greater the difference will be. What you will also be seeing is a heap of stuff from the includes that are only referenced in the source, but have to be pulled in for the binary script. A single function in the original source like
GN_DetermineCombatRound();
will probably result in several hundred lines of added code in the decompiled source.
Giving the 3rd party script a cursory once-over, it looks like he has completely removed events KOTOR_HENCH_EVENT_ON_PERCEPTION (2002), KOTOR_HENCH_EVENT_ON_COMBAT_ROUND_END (2003), KOTOR_HENCH_EVENT_ON_ATTACKED (2005), and KOTOR_HENCH_EVENT_ON_DAMAGE (2006).