Gods, Demigods, Mortals, the Innermost. self-no-self

Do any of the Greek Mythological Gods, Demigods, Deities and mortals told throughout the Greek mysteries have any relation to actual personages as we find for example in relation with other stories?

There are some examples, which are taught on this website:

Heracles (the Cosmic Christ), the son of Jupiter (IO Peter) and Alcmene, performed the Twelve Labors:

https://glorian.org/books/tarot-and-kabbalah/arcanum-5
https://glorian.org/learn/courses-and-lectures/greek-mysteries/yeshua-jesus-iesus-the-jew-zeus

More importantly do all or most of these stories from the Ancient times simply reflect the mysteries to us and are they still useful or relevant to us today?

There are certainly eternal aspects in those old mysteries, that do not change. Other than that, each spiritual tradition is delivered for the place and time, where it is most useful. After the mission of the tradition is fulfilled, it decays and becomes irrelevant, because people and their mentality change with time. According to Samael Aun Weor the ancient mysteries of antiquity at some point stopped to be relevant. People disrespected and threw stones at the priests of the old Pagan traditions towards the end of antiquity. These days we see examples like Canada, where people burn one church after another. This tells us about the relevancy and usefulness of the church today.

Another thing is how we can integrate the apparent contradiction between an Innermost self, God, Creator with the Absolute notion of no-self and non-creation views? My understanding is more like an in-between of no-self and self, no-self as in no egoic self but rather an intelligent principle that has Divinity in its nature (liberated self) freedom from egoic-self (the non-liberated self).

We need to study the spiritual structures and creation myths with our intuition. Contradictions appear in our intellect, because it cannot process Divinity, which resides in higher dimensions than the intellect. Here is the thing: nowadays we are used to process everything intellectually and even with the help of technology. We are used to it as a culture, which is ok. But remember, there were and are people, who are able to become illuminated, able to consciously penetrate and observe such high aspects of existence (and beyond), although they never had access to an intellectual culture as ours. When they were able to do so, all they had was their heart, where they could store these experiences. They did not write it down, they had no forums and no paper to document this. So we should aim towards becoming self-reliant and carry our insights in our hearts, not in our brains. Of course our intellect is the first stage of getting to know mystical traditions, but it's not the goal.

In relation to the Greek Mysteries or any other legitimate mysteries revealed to us through different times, how can we integrate that or identify which stories, symbols relate to which parts of our Being when we attempt to understand their relation through the Gnostic tradition specifically?

Again, comparing one thing to another is a purely intellectual process of our mind. Even if we could draw out a mapping between all tradition in the world, they would neither awaken our consciousness, nor be without flaw. For every thesis that we formulate intellectually, there will be always an antithesis, because we live in a dualistic existence. The higher we can move up with our consciousness towards Divinity though, the less contradictions we will face. So the answer is: meditate and awaken consciousness. Then you might be able to grasp parallels between symbolism, legends and mysteries.
There are statements on this website, like for example, that the Bhavachakra and the Tree of Life both explain our inner and outer existence. But these things are supposed to give us helping perspectives in order to guide the consciousness to its own experience of this reality.