is ati guru yoga part of short thun practice?
Yes. It is also a stand alone practice.
If this ati guru yoga is the most essential possible guru yoga then is it enough that one does only this type of guru yoga? i take "most essential possible" to mean most important...is that correct?
Yes. It is sufficient.
is the short thun practice a kind of preliminary type of practice?
No, it is a complete practice that integrates Ati yoga and Anuyoga. The medium and long thun integrate Mahayoga, Anuyoga and Atiyoga.
i must admit that i have difficulty in 1.understanding rinpoche and 2.understanding where would these practices fit in?
You will get used to Rinpoche's English and his terminology over time. Primordial state = gzhi i.e.basis; presence = mindfulness, dran pa; instant presence, knowledge = rig pa. essence nature and energy = ngo bo, rang bzhin and thugs rjes.
i still see things in a kind of gradual fashion and all my questions stem from this ..
At what point one does this thun practice?
Whenever you have more time. No time, White A; more time, short thun, even more time, medium thun, etc. There is no specific preliminary practice to do in Dzogchen Community. Perhaps one should learn how to sing song of the vajra properly. A sample practice might run -- purification mantra of five elements; guru yoga of white A and Song of the vajra, dedication. This is a pure Atiyoga practice. But Rinpoche has remarked there is no such a thing as "pure" Atiyoga. Why? Because practitioners have needs since we have dualistic vision. Therefore, we need things like Mandarava practice for long life, Garuda for cancer, etc. But the one thing that is indispensable is Guru Yoga of White A.
If you like gradual style, than I encourage you to study for the base level exam of Santi Mahāsangha. Obtain the book Precious Vase.