Why did Tsongkhapa list guru devotion first in his Lamrim while Atisha did not?
Very good question. This is a quote by Lama Zopa Rinpoche that seems to cover this point.


  Lama Tsongkhapa asked Manjushri, “What is the way to achieve quick
  realizations of the path to enlightenment?” Manjushri answered, “To
  purify the mind of the obstacles to realizations and to collect the
  necessary conditions, the merit, to collect extensive merit, that’s
  one thing. The other one is one-pointedly making requests to the
  guru,” that means with devotion. The third one is meditating on the
  path.


Thus it may have been under Manjushri's guidance that Je Tsongkhapa adopted this order.

You are of course right about the order in which the Lamrim points are presented is different in the various Lamrims. While Jowo Je Atisha used Bodhichitta as the first step on the path, Gampopa in his "Jewel Ornament of Liberation" begins with Buddha Nature. While Patrul Rinpoche begins "The Words of My Perfect Teacher" with the precious human life.

Atisha begins his Lamrim after explaining the three scopes with the following verse:

For these excellent beings
Who aspire to supreme enlightenment,
I shall explain the perfect method
Taught by my spiritual masters.

Thus the Lamp on the Path to Enlightenment is primarily addressed to Mahayana practitioners and thus generating the Spirit of Enlightenment is the first step he presents.

Gampopa has a very interesting presentation in "Jewel Ornament of Liberation". Buddha Nature is the primary cause, the precious human life is the working basis while reliance on a spiritual master is the contributory cause.

Patrul Rinpoche's combines 'Reliance on a Spiritual Master' together with generating the spirit of enlightenment and development of Bodhichitta. One of my teachers has explained that the above are three levels of refuge and Patrul Rinpoche uses it as the preliminaries before the introduction of Mahamudra, Chod and Transference teachings.

Since the Lamrim Chenmo is a sutric text it does not go into the tantra except towards the end where Je Tsongkhapa mentions that the disciple has to practice the teachings of the Vajrayana before undertaking the four methods of gathering disciples. However the Vajrayana is a part of the entire path and thus from Je Tsongkhapa's point of view the preliminaries should include guru devotion.

This is explained further in Panchen Chyoki Gyaltsen's 'Easy Path' where each section is divided into the preliminary, the actual meditation session and time in between sessions. This format is adopted by Kyabje Pabonka Rinpoche as well in 'Liberation in you Hands'. In the preliminary, is the primary practice of Guru Yoga and supplication which helps you understand the meditation topic better.

Thus in the Gelug Lamrims following Tsongkhapa the importance on the Reliance on the Spiritual Master being the root of the path is emphasised. This can be best explained by the benefits of relying upon a spiritual master as found in the Precious Master's Instructions Outline to the Lamrim.

The eight benefits of relying on spiritual masters:
* Coming closer to achieving Buddhahood
* Pleasing all conquerors
* Being invulnerable to demons and misleading friends
* The automatic reduction of disturbing mental factors and incorrect behaviour
* The increase of all grounds, paths and realisations
* Never being deprived of a teacher in all future lives
* Not falling into lower rebirths
* Effortlessly achieving all temporary and ultimate goals