The theory is anti-historical, as the author does not attempt to understand the late texts they cite in the context of Buddhist philosophy as a whole. Philosophy is dialectic, and we cannot understand it by taking bits and pieces from texts separated by thousands of years and thousands of kilometers, divorcing them from their context, and making no attempt to understand what they were saying in their time and place.
It is well known that some Mahayana texts embrace the idea of the “self”, and whether this is meant as a mere rhetorical strategy or a genuine metaphysical stance is a subtle matter, which I explore a little more below.
The basic logical problem, which is found commonly among Buddhist authors, too, is the assumption that the five aggregates are primarily an empirical description of the person. Once we define them as empirical realities, we have by definition excluded a “metaphysical” self, and anyone statements about the aggregates unsurprisingly can be read as not applying to a metaphysical self.
But the aggregates were primarily a classification scheme for theories of self. When the suttas are saying the aggregates are not self, they are not saying, “These things, which we all know are empirical realities, are not-self”. They are saying: “These things, which you take in a metaphysical way as a self, are in fact conditioned empirical realities”. It becomes obvious that “consciousness is not self” is specifically referring to the Upanishadic doctrine (i.e. that of Yajnavalkya).
Such arguments are not new or unusual. They have been made constantly for the last hundred years or more, and indeed, for a few decades in the mid-century they gripped the Pali Text Society and hence became mainstream modern Pali scholarship. The Theosophical Society has been a mainstay of these ideas since its founding.
It’s curious that such arguments make such a fuss about the fact that they can’t find the specific phrasing of the doctrine they want to find, i.e. that the Buddha didn’t say “there is no self”. Yet the absence of their own doctrine is passed over.
The Buddha did not say, “There are two kinds of self, a metaphysical and an empirical.” He did not say, “My highest teaching is pretty much similar to what the brahmans are saying”. He did not say, “The idea of Nibbana as extinction is really just a way of pointing to an eternal absolute.”
Why not? Well, presumably because he thought he had it pretty well covered when he said, “all things are not-self”. Instead of taking the plain and oft-repeated statements of the Suttas on face value, they seek out obscurities and odd phrasings that they can read to their will.
Rather than expecting ancient scriptures to say exactly what we want in exactly the form that we want it, we should look at what they actually do say, and sympathetically ask, what does this mean in its time and place? It becomes clear that many of the stock phrases dealing with not-self are meant in an Upanishadic context. The phrasing eso hamasmi is essentially identical with the Upanishadic tad tvam asi and must be an version of it. Moreover, phrases such as so attā so loko can only mean something like the Upanishadic doctrine (“the self is identical to the cosmos”).
I have discussed these matters in more detail in my essay on the Khandha Samyutta:
https://suttacentral.net/sn-guide-sujato#item4
Many translations in the essay are incorrect. For example, the quoted passage from the Mahayanasutralankara includes the epithet of the Buddha, “Plan Without-Outflowing", which is is strange to say the least; but in fact it is a rendering of ānāsrave dhātau “in the undefiled element”. This kind of mistake in a very basic term does not inspire confidence that the author is capable of handling subtle and profound matters.
For those interested, the Mahayanasutralankara passage is found in several languages (but not English) here:
https://www2.hf.uio.no/polyglotta/index.php?page=record&view=record&vid=1131&mid=1945955
And its commentary here:
https://www2.hf.uio.no/polyglotta/index.php?page=record&view=record&vid=1131&mid=1945956
Running the French through Google translate, and referring back to the Sanskrit, the commentarial interpretation makes clear that this is intended as a play on ideas, relying on the Nagarjunian idea of the notions of self (ātman) and individual nature (svabhāva), for which you can refer previous discussions on this forum.
One thing that it is often overlooked is that the Mahayana writers were constantly trying to twist things, to play with words, to look for a new or unexpected angle. This kind of semi-playful speech can’t be read outside of its context. The authors were not making definitive and absolute statements, they were poking their audiences expectations to get a rise out of them.
Let’s say the most outrageous thing we can. Ooh I know, let’s say the Buddha taught the Highest Self! Hilarious! Then when they’re all worked up, we’ll show that what we really meant was not-self all along! 
It’s the kind of thing that Dhamma teachers do all the time. Well I do it, anyway! We can trace this playful treatment of Brahmanical terminology all the way back to the Suttas (AN 8.11):
“Master Gotama lacks taste.”
“There is, brahmin, a sense in which you could rightly say that I lack taste. For the Realized One has given up taste for sights, sounds, smells, tastes, and touches. It’s cut off at the root, made like a palm stump, obliterated, and unable to arise in the future. In this sense you could rightly say that I lack taste. But that’s not what you’re talking about.”
This kind of interplay is a known feature of such texts, the most famous example being Vasubandhu (Asanga’s brother) in his Abhidharmakosa. He wrote the text to appear as if confirming the Sarvastivada doctrine, then when they asked him to write his own commentary on it, his explanations supported the Sautrantikas. The Sarvastivadins were not impressed.
Returning to the Mahayanasutralankara, the text says roughly that the Buddhas, through the path of not-self and pure emptiness, obtain the pure self, the higher self of the self. This is a challenging moment, a point where the sleepy students at the back of the class are meant to wake up.
The commentary then explains that the highest and purest not-self is the Buddhas’ “self”, i.e. their true nature (svabhāva). In other words, the essence of Buddhahood is the absence of defilements (ānāsrave dhātau), and this state of purity and emptiness is what is being referred to here as “the highest self”.
Thus the commentary is deliberately playing with these historically-charged ideas, assuming a sophisticated audience familiar with the EBTs and their teaching of not-self; with the works of Nagarjuna who equated ātman and svabhāva; and with the then-modern Hindu scholars such as Śaṅkarācārya who introduced terms such as paramātman.
Mahayana philosophy is highly anti-essentialist, and this applies not just to metaphysics, but to the meanings of words as well. By training students in wit and word-play, they sharpen their minds and prepare them for philosophical discussions. And they do so, very cleverly, by drawing on the same rhetorical techniques that were found in the Suttas themselves.
This drawback of these approaches is that, outside of these literate and sophisticated circles, it is easy to read the texts over-literally and draw the opposite conclusion. Such is the fate, alas, of anyone in religion who has a sense of humor.
A further comment is required, I think, on the political nature of these sayings. The original quote in the article is an inscription from the Khmer empire, which was a syncretic Hindo-Buddhist culture. Such synthesis was common throughout the Indic sphere in one way or another.
Clearly, from a political viewpoint it is expedient to emphasize teachings that allow for a reconciliation between the major religious groups in one’s realm. We find a similar thing in modern Indonesia, and it is safe to assume that it was quite common. It would not be the first time that a religious doctrine was taken in one way by the philosophers, another way by the populace, and yet another by the politicians.
