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City Model Building Maps: Texture Atlas Tiling or Unwrap?

I have a city model with lots of materials, lots of tiled textures and geometry that doesn’t unwrap very well. Texture atlasing seems like a very efficient way to manage tiled materials, but I can’t find a workflow to automate the process. Simplygon can generate atlases textures when you merge meshes, but only if there are no tiled materials, otherwise it unwraps and bakes the textures out. Does anyone know if there is a way to make Simplygon (Merge) atlas tiled textures? Has anyone used Flatiron or other tools for 3DS Max to atlas their textures and remap geometry for Unreal?
Thanks!
-Donald

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A texture atlas is only going to improve a small part of it, what would be of more benefit is to use fewer materials and objects.