So even if Pacific Games eligibility rules were somewhat less stringent, 16.3 (a) obliged NZF to comply with the Rio 2016 regulations and FIFA Statutes
Sure, but I am not talking about PG eligibility rules so much as the PG eligibility protest rules. New Zealand's compliance with the FIFA Statutes can only be challenged through some kind of protest process. And the key word in 16.3(a) is the word 'and'.
FIFA Rio 2016 16.3(a)
On entering the preliminary competition(s), the Participating Member Associations undertake to:
a) observe these Regulations and, if applicable as per art. 3, par. 2 above, those drawn up by the respective confederation;
This means that the protest processes outlined in the FIFA Rio 2016 regs and the Pacific Games regs are both applicable.
I understand PG regs say protests need to be made several days in advance of the match, but the timeframe for FIFA Rio 2016 regs is for protests to be made within two hours of the match.
So the only way to follow both sets of regs is to follow the PG regs and put the protest in several days ahead of the match. Then the protest would already have been dealt with by the time of kick off so no further protest under the FIFA Rio 2016 regs would be necessary.
In Vanuatu's case they did not comply with the PG protest system therefore they are in breach of 16.3(a) of the FIFA Rio 2016 regs.
Edit: Actually it might be too harsh to say Vanuatu 'breached' that regulation. It's just that the protest was invalid.