Can I opt to disembark on a stop over (if I am a national of that country) before the second leg of the journey? [duplicate]

Nobody can stop you from getting off the plane in Auckland, but your bags will attempt to go to Sydney whether you like it or not! (Although, as Doc correctly points out, they'll be pulled off if you no-show and then you'll have a lot of hassle getting them back.)

However, just because the company paid for your ticket doesn't mean they have any control of it, or that there's anything stopping you from changing it. I would call up the airline flying you from Santiago to Sydney (presumably Air NZ?) and see if they'll let you change your ticket's destination to Wellington, which would be the best of both worlds.

I'm a NZ national, live in Ak and am "well travelled".
Sometimes airlines seem to go insane and go out of their way to be obstructive BUT odds are with "reasonable" airlines you can achieve this OK.

Read jpatokais link re "nobody can stop you ..." . If the tickets are booked and paid for by your company then any repercussions should fall on them - and these are unlikely to be major ones. If the tickets are seen as having been booked by you the airline MAY try to make trouble for you in future. Best case, if the tickets are assigned to you SOME airlines may allow you to put the remaining legs on hold to be used for an equivalent flight in future. This is unlikely but worth at least checking.

If you tell the airline prior to arrival in Auckland that you WILL be getting off in Auckland they should but may not arrange for them to be taken off at Ak for security reasons at least. Worst case it MAY be in the airlines rights to cancel your flight at source if you tell them before you fly that you are not going to 'complete your contract' with the. This is unlikely but MAY be possible. Read the fine print of your tickets.

Based on past experiences: If I was flying eg QANTAS or Air NZ I'd expect them to try hard to do well by me and I'd be reasonably happy to discuss what I was trying to achieve in advance.

But, if I was flying eg Lufthansa I would not dream of giving them the opportunity of cancelling my flight before I had boarded. [Single examples only: QANTAS have given me a free connecting flight when not obliged to when I missed one due to another airline's fault, Air NZ have rescheduled my flight (out of China) when I (stupidly) rang to do so just after it had left (I got my days wrong). Lufthansa have done their very best to strand my daughter mid world 'because they could']

If you end up at Ak with no baggage reclaim arrangement then if you tell incoming customs that you will not be going on to Australia and why and that your bags are scheduled to go to Australia then you can be (99.999%) sure that they will arrange to procure them for you and that there will be (99% likely) no great holdup. With only one bizarre and extreme example I have found NZ incoming customs extremely friendly, helpful and accommodating over dozens of incoming flights over many years. Treat them well, don't get annoyed regardless of anything and you can expect great service. [Yell at them and they will probably still give great service :-) ].