I've been pondering that para too. I think there are three plausible explanations:
1) It doesn't mean anything in particular. In a major policy document, some sections will be drafted, redrafted, previewed, reviewed and cross-checked to within an inch of their lives. See, for instance, the paras on China. Less contentious sections can be slapped together with a good deal less care. I speak from experience on this!
2) The para might refer to the historic differences between Australia and NZ, including the ANZUS circus, NZ not taking up the two additional options on ANZAC frigates, and also not taking up the options on C-130Js in the late 90s. So a reference to recent past history.
3) Alternatively, the Aust government has been trying to sign NZ up to some future joint procurement projects, and NZ isn't playing ball. The ANZAC replacement project would be the obvious one, but there are many other possible contenders. The proposed Aussie OPVs, the replenishment ships that both countries are in the process of ordering, P8s, even the different choices on infantry rifles.
NZ's soon-to-be-released DWP might add some clarity. Or not.
Personally, if NZ can get commonality with Australian equipment, I think it is worth paying a modest premium for. But if requirements differ, or Australian-built equipment is substantially more expensive than what is available elsewhere, I'm perfectly happy for NZ to go its own way. Australian politicians may be willing to buy votes using their defence budget for industrial welfare, but I'd prefer their NZ counterparts didn't do the same.