It definitely will be possible to pay for Economy X over the phone it just can't be done online. I travel on NZ ticketed and NZ coded VA operated flights across the Tasman all the time and have not problems getting economy X seating.

My suggestion is to get the VA PNR (which should be similar to the EY one or might even be the same) and then call asking for seats to be selected in your preferred economy X seat (do a dummy booking and see what seats are free). When they select it they'll most likely tell you that you'll need to pay and that's when you can pay and select that seat.