There is some discrepancy, but not as much as there may first appear to be.
First of all, we acknowledge that there is some development of the consciousness that can happen mechanically through nature. We are not denying the basic fact that an animal has a greater degree of consciousness than a plant (and the plant, greater than a mineral), and that this development occurred through a mechanical process.
Moreover, the development of different faculties in successive incarnations of the earth is a teaching also found in the works of Samael Aun Weor. He talks about this in The Revolution of Beelzebub. Specifically, the bodies of man are developed in pairs. At the start of this Cosmic Round, in the Saturnian Epoch, the present humanity had only the physical (in a germinal state) and the Spirit. Next, in the Solar period, our humanity received the vital and Buddhic bodies. In the Lunar period, we received the Astral Body and the Body of Willpower.
He does not mention the development of a body in the current Terrestrial period explicitly, but it is easy to extrapolate that the remaining body for man to receive is the Mental Body, the development of which corresponds to humanity developing intellect.
Here are the quotes I'm referring to, and the chapters where they can be found, in case you are curious:
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**Saturnian Epoch
At that time, our modern human bodies were only germs with the possibility of unfolding. ("The Two Ways")
The present human “Innermosts” (Spirits) were just virginal sparks who were animating the mineral kingdom. ("The Two Ways")
** Solar Epoch
The physical bodies of our present humanity were developed a little more and these bodies received the Vital body, which in the present time serves as a foundation for the whole human biology. ("I Accuse")
When the cosmic night of the Solar epoch approached, after millions of years, the Four Lords of Flame endowed the present human Innermosts (Spirits) with a Spiritual Soul or Buddhic body, which is the body of intuition. ("The Atom Nous, The Solar Period")
** Lunar Epoch
During the Lunar period, the physical bodies of our present humanity reached a high degree in their perfection. We acquired the Astral Body during that period. ("The Lunar Period")
The Innermosts (Monad-Spirits) of this present humanity acquired the body of the Human Spirit, called the Body of Willpower, which Krishnamurti despised so much. ("The Lunar Period")
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If you follow the pattern on the Tree of Life, you can see that the development is proceeding in two directions: From the Spirit, moving down (through the Divine Soul and Human Soul), and from the physical, moving up (through the vital body and astral body). And the two paths connect in the mental body. But once you receive the mental body, that's it. There are no more bodies to be developed by nature. There are other faculties and stages of development, but those are not accomplished mechanically.
It can be easy to make the mistake that our development may continue mechanically. Simply by looking at past progress and extrapolating, one might be led to believe that the trends we have observed in the past will continue indefinitely. However, this is akin to observing a child over time and saying, "This child has grown taller every year. He must continue to grow taller forever."
In reality, nature never moves strictly in one direction. Everything in nature moves in cycles, and what today is built up, tomorrow will be broken down.
So the teachings of Samael Aun Weor do not disagree dramatically with those other teachers in terms of the historical facts. Rather, the difference is in Samael's recognition of a fundamental law of nature, and the implications of that natural law for the process of evolution (and devolution).