Hey Chiyu, I did some research on the Arcologies and how they overlap and I made an interesting discovery:
In the original Next War mod, if you use the World Builder to add the different arcology types, it results in 3 domes around your city. Now, that, at first, appears to be their intent, but if you actually play through and build the buildings during normal gameplay they do in fact remove their prior forms, resulting in a single dome (with shield graphics). So their original intent was always to simply apply shielding graphics to the pre-existing Arcology.
Looking further, I inspected each city after each building had been built. It appears that when you build the shielding the entry for "Arcology" in the building list disappears and is replaced by the Arcology Shielding or Advanced Shielding entry. I'm certain there's something in the Python that causes this behavior.
Also, there's some strange quirkiness with the bonuses that the Arcologies give you. The first Arcology grants +3 Health. The second grants +1 Happiness (no health) and -25% Gunpowder and Nuke damage, as well as +1 trade route. The third grants +1 Happiness and +1 Health and -30% Gunpowder and Nuke damage, and +1 trade routes. It seems to me that they intended the older buildings benefits to be carried over to the new building and improved, so the 25% becomes 30% and so on, but this isn't carried from the original Arcology's +3 health to the ultimate +1 health - which seems odd to me. It appears that the real benefit Advanced Shielding should grant is -30% Gunpowder and Nuke damage, +1 or +2 trade routes, and either +5 Health and +2 Happiness or +3 Health and +1 Happiness. Currently the advancement to shielding makes you lose health! I don't think that was their intent.
Anyway, I just wanted to share my small research and opinion on the matter in hopes you'll include this function in your mod. Thank you, and again, great work.