Richard
I guess I just assumed he would want a 'correct order' because of the later positioning of the fool before the world, but I suppose that's unrelated to what he's saying in this part.
In PKT Waite discusses the Trumps in the Levi ordering (almost), because this was customary at the time. However, he does not think that the Fool belongs in that position, nor should it be the final Trump.
Waite said:That which hereinafter follows should be taken, for purposes of comparison, in connexion with the general description of the old Tarot Trumps in the first part. There it will be seen that the zero card of the Fool is allocated, as it always is, to the place which makes it equivalent to the number twenty-one. The arrangement is ridiculous on the surface, which does not much signify, but it is also wrong on the symbolism, nor does this fare better when it is made to replace the twenty-second point of the sequence.
ETA. Waite may have changed his mind later about whether there is a "correct" ordering, but I think I can prove that his stance in PKT is that there is indeed a preferred order. Otherwise certain of his statements make no sense whatsoever.