fwiw, i think the decision to sample the sounds as pure as possible with the swell box fully open was an excellent decision as the vi would have been too unwieldy otherwise. in compensation though, i think it would be a mistake to underestimate the value of filtering when considering how volume effects are created on the organ. for those unfamiliar, the organ is constructed in divisions of pipework associated with each of its manuals (keyboards). these divisions are either "exposed" as in the pipes we can see in the room, or "enclosed" in chambers (small rooms) that can be gradually closed off by louvers that look like vertical blinds called shutters. the shutters gradually open or close via a volume pedal at the organ console.
because a reduction in volume occurs as a result of obscuring the sound by placing it in literally in another room, it becomes important to simulate that effect with a low pass filter rolling off higher frequencies. at no point on the organ is it possible to have the pure unobscured sound of the enclosed divisions, but with the shutters closed, any more than it is possible to have the brassy effect of a horn sound at pianissimo.
to the extent that it would not have been desirable to sample the organ with multiple layers for the enclosed divisions, i think it becomes even more important to note that the primary association we have with an organ's swell effect is its reduction of high frequencies as the shutters restrict the sound, and only secondly the actual change in volume. further, it seems important to note that considerable sound still escapes from a fully enclosed chamber (volume can't ever be reduced below perhaps fifteen or twenty percent) and composers routinely call for this restricted sound (not just as an effect) in the repertoire.