THREAD: It might really be that Game Freak sees Moltres as the central bird, because even Silph Co.'s Porygon has Tri-Attack with Fire in the middle corner of the triangle in most of the move's depictions.
Also:
Articuno > Winter
Moltres > Spring
Zapdos > Summer
Ho-oh > Autumn https://twitter.com/Nintendokusou/status/1240696421663141899

This could make sense with the Right Pillar being Energy and Expansion based and designating the Summer Solstice (Zapdos), and the Left Pillar being Form and Contraction based and designating the Winter Solstice (Articuno).

Then there's the Middle Pillar, which is Spirit and Balance based, with Kether designating the Spring Equinox (Moltres), which is when things are born, and Malkuth designating the Autumn Equinox (Ho-oh), which is when things die to later be reborn anew.

Interestingly, while the GS Prototype supports this by only including Ho-oh, then Lugia was later introduced due to a request for the Movie 2000, and ended up becoming Ho-oh's opposite and linked to Spring too, so in a sense it could represent the Soul's rebirth after its death.

This would further explain why the Burned Tower is now linked to the story of the symbolic deaths of Rai, En and Sui as beta prototype Pokémon which were reborn in the final games as the Three Sovereigns, Rai-kou, En-tei, and Sui-cune, via Ho-oh's powers.

To complement this, Ho-oh is tied to Sacred Fire, which symbolically burns and purifies the dead matter associated with Autumn into Sacred Ash, the Alchemical Salt, which is then recycled, transformed, and incorporated into the new matter associated with Spring, as Lugia implies.

This also explains the visual cues of the Kimono Girls to the Spring and Autumn Equinoxes and of the Furisode Girls to the Summer Solstice, while suggesting a future group will show up in Gen 9 that is linked to the Winter Solstice and has the two remaining Eeveelutions.

Finally, Moltres being the central one also explains why it's the central head of ZapMolCuno (Thu-Fi-Zer) and was the one chosen to learn Sky Attack (JP: God Bird), which might even imply their fusion might have once been what Ho-oh became, the "God Bird".
https://bulbapedia.bulbagarden.net/wiki/Legendary_birds_(Adventures)#Thu-Fi-Zer

Now the weird part is that while their beaks match the ones seen in the heads of Python Mercurius depictions, they gave Mercury to Zapdos when it should be Sulphur, and Sulphur to Moltres when it should be Mercury, at least if the trio logic described previously was the intended.

The other weird part is that sometimes they seem to imply this idea that Zapdos is the actual central one, like we can see in some recent artwork, even though the game logic suggests that Moltres is the central one, as we just saw above. It's hard to figure out at certain points.

Moreover, in the context of the Crown Tundra, if the G-Winged Mirages end up being a representation of the Three Jewels to complement Calyrex's role as a Bodhisattva figure, then it would make sense for Zapdos to take the central role as the Yellow Jewel.
https://twitter.com/Nintendokusou/status/1248456359189680129

All in all, Pokémon is complicated to interpret correctly, and sometimes I really wish I could sit with each of the individual developers and ask them "what's the deal with these guys?" to get a more clear answer.
Still, I really need to replay all the games again... one day...

Was here re-pondering my two versions of the Tree of Malkuth according to what I was talking about above.
The left one seems to tie in better with the Gen 1 and 2 games, plus related movies, etc., while the one of the right seems to tie in better with the franchise's development.

Left Version Summary:
- The Winged Mirages have been clearly depicted as the Trinity in several occasions, so makes sense for them to take the top 3 spots as shown, and that's even supported by the recent LGPE paintings in the office of Silph Co.'s President.

- In the same office, Giovanni places Dr. Fuji's research documents on the desk at the center, and these are implied to have pictures of Mew and Mewtwo. These two are tied to red and blue auras in Mewtwo Strikes Back, as they take on opposite view points. https://twitter.com/Nintendokusou/status/1240698121698471936

- Ho-oh, Lugia, and Suicune have ties to Gold, Silver, and Crystal, plus the Sun, Moon, and Earth, and these are the minerals and planets associated with Tiphareth, Yesod, and Malkuth. Besides this, they are obviously the three cover mascots.

- The 3 Sovereigns are linked to the incident of the Burned Tower, which is tied to the symbolism of the Path of Peh and "The Tower" card (a.k.a. The Lightning-Struck Tower), so Raikou and Entei take both poles of that path since they represent the elements that destroyed it.

- Both Entei and Raikou are also linked to Crystal in different ways. Entei is the "Emperor of the Crystal Tower" from M3, caused by Unown's illusion of material reality, while Raikou destroys the Miracle Crystal from "Legend of Thunder" to protect many Pokémon from Team Rocket.

- Finally Celebi is called "the Voice of the Forest" in M4, and Daath can be linked to the Vishuddha Chakra and the Throat, which are linked to this power of the Voice and Spoken Word. Daath can also be seen as a portal to other times and dimensions, relating to its time-travel.

Right Version Summary:
- This one is more based on generic and transpersonal archetypes these Pokémon have taken on over time. Ho-oh and Lugia take over Chokmah and Binah as the Sky and Sea Guardians, and act as the King and Queen of their respective Solar and Lunar triangles.

They also gain other aspects from these Sephiroth in M20 and M21, like how, for example, Lugia becomes known as "Wind Lugia", taking on properties associated with the Holy Spirit which is many times described as a wind.

- Mew makes sense in Kether since its DNA contains the genetic code of all Pokémon and it's thought to be their common ancestor, while Mewtwo makes sense in Malkuth as the latest Pokémon yet one disconnected from Spirit due to it being engineered and lacking proper understanding.

Their Chinese names further suggest this by calling Mew a "dream" and Mewtwo the "ultimate dream", so in other words, the first original principle and the final altered result based on the former.

- The 3 Sovereigns are now embodiments of the Compassion of Water, the Passion of Magma, and the Speed of Lightning, which seem to match Tiphareth as the Pure Compassionate Heart, Geburah as the Umpredictable Slumbering Volcano, and Chesed as the Jupiterian Lightning Deity.

Also notice the red and blue in Entei and Raikou's faces.
Suicune becomes the central aspect of this Tree of Malkuth due to its connection to Sandalphon, as the Crystal Princess, and the High Priestess, who stands between the pillars and guides the initiate through the mysteries.

- Celebi remains mostly unchanged, although M23 could add to it.
- The Winged Mirages, in this case, are more associated with the characteristics of the locations where they can be found in the games in relation to their respective Sephiroth.

- Articuno seems to match up with Hod as the frozen Temple of Ice, plus the Seafoam Islands are described as twins, suggesting a link to Gemini, which is ruled by Mercury, the wielder of the Caduceus, with its twin serpents.

- Moltres seems to match up with Netzach as Nature's Creative Fire, in part due to its link to Spring. It's also found in Victory Road, matching Netzach's victory over adversity theme and its tool of the lamp, as Victory Road is covered in torches in LGPE, even around Moltres.

Mt. Ember has tones of that, since it glows at night due to Moltres, but it also has links to Geburah because of the Ruby.
- Zapdos seems to fit Yesod's "Vision of the Machinery of the Universe" as it can be found at the Power Plant, later used to provide energy to the region.

In closing, I just want to say that this is my current interpretation and it's subject to change in the future, as this is a very complex topic and if we look at the Tree of Life as a dynamic system, which we should, it becomes hard to establish concrete associations sometimes.