Well, MOS wasn't filmed in Imax (and it doesn't appear to have special scenes using the Imax format). So it would have to be converted, rather than genuine.
And WB bullied Zack to having 3D conversions. So, he decided to film some parts in a manner that reflected the inevitable, so that it would look a little better than one that was shot as a strictly 2D film.
Since his only 3D film before was a CGI owl movie, I can only assume that he's not fond of 3D (he still shoots on film), and bent to studio pressure. On the bright side, there will probably be a bigger box office income as a result.