Philosophically speaking, what's wrong with this argument? In ek the pilots (and all other workers) rely on the benevolence of management to change terms and conditions, flight time and duty limits, fatigue management and pay. Generally speaking managers will always provide the minimum in these areas because their mandate is maximum profit.
Given that this is the case then a lack of workers willing to engage with the company because they feel that items of the whole package are not up to scratch would lead to managements having to address the issues that need resolution. Personally my beef is mostly about fatigue and FTL issues and the long term viability of a job with ek.
It follows then that a group of pilots who are still effectively employed by another company (although not being paid) and who have some labour representation will work against the interests of the larger group. I assume also that the ANZ contract chaps will still be represented by their old union as they still have links to ANZ.