Very interesting article. Some thoughts (excuse my bombast but I don't have a filter):
1. people (white northern European Protestant to be precise) have this idiotic notion that everyone in every tradition were of one mind on doctrine etc. For some reason they have no clue that crypto-faith was dominant in all traditions at all times other than wholly ignorant white population that began as barbarians. Just as there was kabbalah among the Jews - even the very Jewish leaders who condemned kabbalah - no surprise that these monks could have been of another mind regarding orthodoxy.
2. when he writes "[o]n the evidence of those texts that have been preserved in multiple copies, like for instance the Apocryphon of John, the textual differences between the exemplars indicate that we are here deal-ing with a form of 'living literature' , i.e., literature that has been con-tinually rewritten to fit changing contexts and circumstances. This again implies that a focus on authorship and on an original text is misguided, and that analyses that are based on our best guesses regarding the individual texts’ Greek originals, or Vorlagen, are, by their very nature, highly speculative. I would therefore instead advocate an approach more in line with “new philology”, where variants are treated as the norm rather than as deviations, with a sharper focus on the Coptic texts and their manuscripts as we have them" - WTF is wrong with people again? Why is it such a shock that there were ur-texts which were continually adapted by later scribes in early Christianity? The canonical gospels are the obvious example (unless you are a pious ignoramus). But consider the Patristic texts too. Tertullian's entire corpus is a recycling of Justin, Irenaeus, Theophilus. With respect to Justin the Against Marcion Book 4 and 5 attributed to Tertullian is CLEARLY and OBVIOUSLY a retread of something originally written by Justin or someone in his circle (the Galatians-first Pauline canon tradition with one gospel harmony) reworked by Irenaeus to redirect the work 'Against Marcion' and finally translated loosely into Latin by Tertullian. Similarly Against Marcion Book 3 was written by Justin against Jews (cf. the parallel sections of Against the Jews by Tertullian). Many have put forward arguments that Book Two was originally written by Theophilus and certainly Against Hermogenes was written by Theophilus (look at the stupid part where Hermogenes being in Antioch). Irenaeus has been noted to recycle Theophilus and Justin. Most suggestive of all is Eusebius and later Rufinus's reworking of Origen. The point is that it is hardly surprising what he is suggesting. It runs up against the stupid people mentality that 'the gospels were written by the gospel writers' (even though the Marcionites denied this in antiquity), 'our Pauline corpus was written by Paul' even though the Marcionites had a different recension and the Pastorals are fake etc. etc. Great point he makes but it is amazing it should be controversial in the first place - only shows the retarded nature of scholarship that we should be shocked by the assertion.
3. I've long noticed interpolations he is suggesting in the Testimony of Truth (not sure what codex that's in). It appears to me that an orthodox scribe has added many glosses. First, notice the interpretation of the parable of Jesus in the manner reported by Hegesippus:
And they show that they are assisting the world; and they turn away from the light, who are unable to pass by the archon of darkness until they pay the last penny.
So the interpretation is ancient. But then this (italics) is a later interpretation:
When the [...], he grasped him, having bound him upon [...], and he was filled with wisdom. He bore witness to the truth [...] the power, and he went into Imperishability, the place whence he came forth, having left the world, which has the appearance of the night, and those that whirl the stars in it. This, therefore, is the true testimony: When man comes to know himself and God, who is over the truth, he will be saved, and he will crown himself with the crown unfading.
John was begotten by the World through a woman, Elizabeth; and Christ was begotten by the world through a virgin, Mary. What is (the meaning of) this mystery? John was begotten by means of a womb worn with age, but Christ passed through a virgin's womb. When she had conceived, she gave birth to the Savior. Furthermore, she was found to be a virgin again. Why, then do you (pl.) err and not seek after these mysteries, which were prefigured for our sake?
It is written in the Law concerning this, when God gave a command to Adam, "From every tree you may eat, but from the tree which is in the midst of Paradise do not eat, for on the day that you eat from it, you will surely die." But the serpent was wiser than all the animals that were in Paradise, and he persuaded Eve, saying, "On the day when you eat from the tree which is in the midst of Paradise, the eyes of your mind will be opened." And Eve obeyed, and she stretched forth her hand; she took from the tree and ate; she also gave to her husband with her. And immediately they knew that they were naked, and they took some fig-leaves (and) put them on as girdles.
I would argue that the italicized material disturbs the flow from the argument which precedes it (i.e. knowing oneself) and eating of the fruit (cf. 'it is written in the Law concerning this
" = knowledge). Have to go.