Based on my reading of Pike and the history of the Scottish Rite (which certainly is not exhaustive, by any means), Albert Pike viewed Masonry as an organic whole, with each modern iteration of it representing to a greater or lesser degree the pure Masonry lost in its own pre-history. Pike believed the AASR captured the essence of true Masonry and that other "rites" did so to a lesser degree, but the sum and substance was hidden in the Blue Degrees.
Pike believed (and it's still reflected in the teachings of the Scottish Rite) that the Blue Degrees with their elaborate symbology and ritual were purposely designed to conceal, not reveal. So, in that sense, when the anti-Masons claim that the "truth" of Freemasonry is hidden from the the holders of the lower degrees, they are correct. Where they are in error is in what they believe is being hidden.
Pike believed, and the Scottish Rite teaches, that the sum total of Masonry can be found in the symbology and ritual of the Blue Degrees. But by design the sum is never taught in the Blue Lodge. Pike believed true Masonry always involved more than the first three degrees as given; these are just the entryway. What Pike lamented is the belief that what is given as given to the Mason in the Blue Degrees represents the truth of Masonry on its face. Pike believed the teachings of the Blue Degrees as given had one end: to prod the Mason to look behind and beneath the surface of those teachings to find the treasure within. And he believed the Higher Degrees of the AASR were the most suitable pathway to that treasure.
I believe the current notion of the Scottish Rite as being an "appendant body" to Masonry would have been foreign to Pike. Keep in mind that while not generally practiced, the Scottish Rite has its own versions of the first three degrees, and is, therefore, a complete system of Masonry unto itself. And I believe that is the way Pike viewed the Scottish Rite. It was, for him, Freemasonry in its most unadulterated form.