Thank you so much for the detailed reply. and for taking time to explore my work. If you are interested, my portfolio has some artwork i did using either flat or gradient textures: https://bukkbeek.github.io/
Similar to you, I used colors/ gradients to match the aesthetics I'm going for. But then I wanted to make a universal palette:
This is one of my gradient palettes:
But this did not live up to my expectations as I had to tone it depending on the project. For example this following airship used a less saturated one: https://sketchfab.com/3d-models/nomads-barge-wandering-airship-of-elysium-7192f9...

This also has a flat version as well:

In all, I maintain a material library to use from if these are not enough (specially for grounds/ camo), then I bake it:

But I think this final palette still needs a lot of refinement as I ended up using some colors many times and some never used at all.
On the other hand, I was thinking an approach similar to your idea as well, having a bigger single atlas and build colors as I go.
That's how I approached making my portfolio game: REBEL.101 by Bukkbeek using following texture: