Here is a quote by Khenchen Thrangu Rinpoche that is relevant,
In the case of deity meditation, it is the mind consciousness that creates the body of the deity. It is thus a mentally created body, and thus, so to speak, unreal. When, however, the karmic imprints of this visualization get stored in the all-base and become more clear and more stable, it is actually possible to meet the deity one day, or Guru Rinpoche, for example, face to face! This is the result of deity meditation with in-front visualization. [From Everyday Consciousness and Primordial Awareness, p. 39]
Here is an interesting comment, also by Thrangu Rinpoche, on the notion of "external" objects and the all-base/ground consciousness,
There are two kinds of objects: objects that appear clearly and vividly to the six consciousnesses and objects that reside in the ground consciousness as latencies. When we perceive things in a room, there are also many other things outside the room that we cannot perceive. Where are they? They are in the ground consciousness, not as objects but as latencies. When we leave the room, then the room and the things inside it remain in our ground consciousness, since they are no longer appearing to any of the six consciousnesses.
The ground consciousness is vast in terms o the objects contained within it. The whole world is contained in the ground consciousness in the form of latencies. We can go anywhere in this world, and that place will appear, will become a vivid appearance, because everywhere we can go is already present as a latency in the ground consciousness. [From Ocean of Ultimate Meaning, footnote 3, page 182]
From this perspective, it's all
imprints, even actually appearing deities.
Though these are both interesting quotes, I think they're actually addressing different issues. The first alludes to the difference between the samayasattva and the jnanasattva, while the other has to do with how appearances manifest from the alaya. As for your conclusion, it's not that the deity is an imprint, but only how it appears to you that could be characterized as such.
As for the OP, it certainly is the POV of Vajrayana that Vajrasattva is an actual enlightened being that made aspirations that his mantra would purify the obscurations of sentient beings, hence its effectiveness. As Tsoknyi said, "he is not nonexistent," like the horns of a rabbit, which other than on jackalopes, do not exist at all. However, that does not mean that he exists in the way theists, Hindu or otherwise, ascribe existence to their deity. More importantly it is the POV of the Vajrayana that to truly understand the nature of Vajrasattva one needs to purify obscurations. And the quickest way to do that is said to be through the recitation and meditation of Vajrasattva.
On the other hand, I think this question is indicative of the tendency of modern westerners to find the more profound persecpectives more palatable. In other words, we'd rather view the deity as symbolic of our own mind than as an external entity. Unfortunately this is more of a sign of our lack of trust in the teachings, than it is of our superior understanding. It is far better to work with our dualistic experience in a constructive way, than to pretend we experience nonduality and thus grasp the more profound and subtle perspectives, when in fact we don't.