Zen? A separate transmission? No....Yes....
Here is a little contribution given in the hopes of stirring some of you all into sharing your views (or non-views).
Though Dogen used the terms "Zen," "Zen sect," "Zen ancestor," etc. he consistently maintained that Zen was not a school or sect of Buddhism, but was the authentic transmission of Buddhism itself. In this sense, Dogen’s use of the word "Zen" ("Zen," "Zen sect," etc.), can be thought of as a term that simply means "Buddhism."
Verification of this can be seen in one of the hallmark characteristics of Dogen’s Zen teaching: his insistence on the inclusion of the Mahayana scriptures and treatises, as well as the koans and records of Zen masters. The notion that Zen was a "separate transmission outside the teachings" (scriptures, treatises, Zen records, etc.) was seen by Dogen as an aberration.
When we regard Dogen’s work with his perspective the authentic Buddha-Dharma, his expressions become much more discernable. Dogen’s writings are masterful expressions of what he called the "rightly transmitted Buddha-Dharma." They are not a "new and improved" school of Zen. That is to say, Dogen’s teachings can only be understood when appreciated in their proper context: the traditional teachings of Buddhism, both Hinayana and Mahayana.
His manner of expression was fresh, provocative, and ingenious, however the reality, which his expressions were intended to indicate, was the identical reality that was realized by the historical Shakyamuni Buddha. In Shobogenzo, Bukkyo, Dogen describes in detail exactly what he means by the rightly transmitted Buddha-Dharma:
"Some fellow has said, "Old Man Sakyamuni, besides expounding the teaching and the sutras throughout his life, also authentically transmitted to Mahakasyapa the Dharma of the one mind which is the supreme vehicle, and this transmission has passed from rightful successor to rightful successor. So the teaching is opportunistic idle discussion, but the mind is the essential true reality. This authentically transmitted one mind is called ‘the separate transmission outside the teachings.’ It is not to be likened to discussion of the three vehicles and the twelve divisions of the teaching {sutras and shastras}. Because the one mind is the supreme vehicle, we speak of ‘direct pointing into the human heart’ and ‘seeing the nature and becoming buddha.’" This expression is never about the everyday conduct of the Buddha-Dharma: it lacks the vigorous road of getting the body free, and it has no dignified behavior throughout the body. Fellows like this, even hundreds or thousands of years ago, were proclaiming themselves to be leading authorities; but we should know that, if they had such talk as this, they neither clarified nor penetrated the Buddha’s Dharma and the Buddha’s truth… The reason they say that [buddhas] authentically transmit only the one mind, without authentically transmitting the Buddha’s teaching, is that they do not know the Buddha-Dharma. Not knowing the one mind as the Buddha’s teaching and not hearing the Buddha’s teaching as the one mind, they say that there is the Buddha’s teaching outside of the one mind… Although they have transmitted and received the fallacy of "a separate transmission outside the teachings," because they have never known inside and outside, the logic of their words is not consistent. How could the Buddhist patriarchs who receive the one-to-one transmission of the Buddha’s right-Dharma-eye treasury fail to receive the one-to-one transmission of the Buddha’s teaching? Still more, why would Old Man Sakyamuni have instituted teachings and methods that could have no place in the everyday conduct of Buddhists? Old Man Sakyamuni intended, already, to create teachings and methods to be transmitted one-to-one: what Buddhist patriarch would wish to destroy them? Therefore, the meaning of ‘the one mind which is the supreme vehicle," is just the three vehicles and the twelve divisions of the teaching, and is just the Mahayana treasury and the Hinayana treasury… Therefore, do not, through belief in the fallacy of "a separate transmission outside the teachings," misunderstand the Buddha’s teaching.
~Shobogenzo, Bukkyo
Source: Zen Master Dogen's Shobogenzo, Translated by Gudo Nishijima & Chodo Cross