After more consideration of this quote, I believe I understand it now. To paraphrase no. 1:
"1. the obscuration of certain details in the symbolism (in the Waite-Smith), so that captious critics might find reason for doubting the (our) interpretations;"
He seems to be saying that Waite intentionally obscured some of the symbolism in the Waite-Smith, which the BOTA version clarifies. Case's system was starting to have major differences from the Waite-Smith imagery and he felt the redraw was necessary to avoid criticism from those who would say his interpretations didn't match Waite's symbolism. Fair enough. In his following paragraph he uses as an example of the Lovers. The flames on the tree behind the man, he says, should each have a triple flame; but this isn't obvious in the Waite-Smith, so the BOTA version has clarified it. Another example he gives is the iris flowers in Temperance, which, he says, Waite uses as cover (not Case's exact word but implied) for the rainbow. But he seems to be assuming a lot. It's quite possible the flames on the tree were never intended to each have a triple flame; and likewise, the iris flower does have a connection to the rainbow, but to say Waite has used it as camouflage for a rainbow takes the symbolism in a direction Waite may never have intended.
And no. 2:
"2. the alteration of other Keys (by Waite), so as to make them expressions of Dr. Waite's personal ideas, rather than correct statements of their original meaning."
"Original meaning" is a little vague and I'm not sure what he's referring to. The subtitle of Waite's
Pictorial Key is, "Being Fragments of a Secret Tradition Under the Veil of Divination." This was his position,
i.e., the trumps were keys to the Secret Doctrine. It didn't have anything to do with his personal opinion, at least not as far as I can tell. For Waite the Secret Doctrine wasn't anything that could be learned from books or occult schools, and it certainly wasn't a matter of personal opinion; it was something taught by God directly to the soul:
"The existence of a concealed doctrine of religion perpetuated from antiquity cannot be proved by recourse to Kabalistic literature, and in so far as this notion has been rested thereon, it is to that extent discounted, yet the question itself does not stand or fall by the Kabalah. Speaking from the transcendental standpoint for the first time, as I feel warranted to do in concluding, I venture to say that it is in Christian channels that this doctrine must be sought by those who assume it, by which I mean that the transcendental succession has passed into the Church of Christ. The question, however, is not approachable from the historical side, and in no real sense of the term can it be said to possess such a side. It is therefore outside the common channels of inquiry, and assuming for the moment that any person now living in the flesh is entitled to affirm its existence, then he best of all, though not he only, is aware that the secret doctrine is not of this world."—Doctrine and Literature of the Kabalah, 1902, (final chapter last paragraph).
Case's system is supposedly a "key to the Wisdom of the Ages," or more specifically, occult science. It's not bad as far as that goes, I've gotten some good insights from him. But the impression I get as I read him is he believed Waite was trying to conceal the secrets of occult science in the Waite-Smith tarot, which could not be further from reality in my opinion. He tries to fit Waite into
his mold.