No, the flights, etc, happened after NZF had received the transfer request, he actually didn't leave the UK until the 4th which was after the window closed so I wonder if NZF had swept under the carpet the transfer issues even back then. They would have known that they missed the deadline.
So timeline:
Phoenix submitted the paperwork to NZF on the 30th
They announced the player on the 1st (Simon Hampton wrote an article saying that the Phoenix shouldn't have announced the player until the paperwork cleared, but that seems a bit harsh if the extent of what NZF needed to do that has been speculated is correct)
The window closed on the 2nd
NZF submitted the manual paperwork on the 3rd
The player left for NZ on the 4th, at this point NZF and presumably the Phoenix would have known that there were issues.
Arrived in NZ on the 6th
It was announced that there were issues on the 11th
The decision was declined on the 16th
Alex left on the 18th and is now on a stop over in Sydney.
So what happened between the 3rd when they knew there were issues and the 11th when the fact that there were issues was announced? And why did the player even get on a flight when it would have been clear that there was going to be a problem from the 3rd and everyone who knows anything about FIFA knew it was a certainty that the loan agreement would be declined?
So either the Phoenix were incredibly naive or NZF weren't being honest with them.
I'm willing to give NZF the benefit of the doubt here, that the poor admin staff person who had never been trained to use the system, and had this task thrown at them didn't realise just how unmovable FIFA is so assumed that sending a fix the next day would be acceptable. But the fact is that there was still time to stop Alex from even wasting his time by getting on a flight.