I wonder if this location move is part of the prior announced budget tightning and this portion is just now coming to light? Seems like it could be. I doubt this is a reduction from their stated cost goal of $140m.
Like the piece said a number of productions already do the establishing shots and then film interior photography elsewhere. If I were on the NYC film board I'd look into all the revenue they are losing. Obviously it's too costly, hence why Nolan likely used price as a reason to not shoot his Batman movies there. No one would say those films suffered, hell his movies clearly show Gotham is not NYC here at least they are going to visually make it obvious still that Avengers is in NYC based on exteriors.