Hello Ray,
The problem is that if the phases of the tremulants recorded in the audio samples were to be aligned then one would either have to use an artificial amplitude envelope for the pipe attacks and releases, instead of real sampled pipe attack/releases (which I think would involve a significantly greater loss of realism than non-synchronised tremulant phases), or one would have to delay the speech and release of each pipe until its sampled tremulant phase matched those of other pipes sounding at the time (which could introduced a large and variable latency/jitter, e.g. up to 1/2 second for a 2 Hz tremulant). Personally I don't think either would be acceptable to most people.