I could explain what my issue is, but I fail to see the relevancy. I am asking for help on how to escalate this, not to justify why it is an issue for me, to hear on the process of importing, or to hear on the benefits of prepaying. If you do not have a useful response to my query - please, don't waste your time going off on tangents.
Your issue is very relevant, because based on what you've posted eBay are doing things 100% to the law following IRD's processes.
You claim "If I buy one item that is >NZ$1000, the checkout correctly does not add GST - if I buy several items from the same seller and the combined cart total is >NZ$1000, it adds on GST when it should not do this."
If multiple items under $1000 are sold together in a single transaction that totals over $1000 eBay need to add GST because IRD tell them to. Your view that they shouldn't be doing this is incorrect.
eBay can choose to collect GST on high value items (single items over $1000) or they can choose not collect GST which results in the high value item being processed by Customs here in NZ. To make the whole purchasing process better for 99% of their customers both eBay and Amazon collect GST on high value goods so the end customer in NZ doesn't have to deal with Customs or a customs broker here in NZ.