Yes the works were recorded by two (I think) different engineers based on the event, but cannot recall specifically microphone placement. I will say at their closest, particularly for solo organ, the placement is on the nave floor a good distance from the cases. The lack of resonance also has to do with the fact that the room was packed to the gills for the Inaugural Concert (Stanford, RVW, Paulus), and Recital (Latry) which does affect the sound even when in the room. The local music critic reviewing events at the church kept commenting on the deadness of the room which was not a wholly true statement. If you take the pew cushions out of the church you add almost 2-3 seconds of reverb which becomes nearly too much.
The Nestor anthems were recorded live in worship and the organ solos (Bolcom, Sowande) re-recorded after worship due to pre and post service socializing.
I too think the Paulus made a better, even bigger impact in New York. Maybe it had to do with programming as well as the "state" of the piece when first performed. It was exciting to be on the receiving end of something which I had been somewhat involved in - page turner!
(now of Highland Park Presbyterian, Dallas, TX)