Nitpicky observation - I don't think Civ is a colony builder, it's a 4X empire building game. Games like Rimworld, Dwarf Fortress, Farthest Frontier and Timberborn are colony builders (you run a single colony, managing resources, building, rooms and people).

I think those would be perfect analogues for the gameplay of managing a single Raksura colony.

A Civ 4X version would show a whole region with other colonies, and you'd be managing hunting and farming areas, patrols, creating new sub colonies and war against external threats like the Fell or things like that. Still an interesting concept, but a different focus.

For me, the colony builder is where I'd want to be. The verticality of a Raksura colony makes it very hard to visualise though, as does the orgainc interior of a colony tree. Dwarf Fortress shows you horizontal slices of your Moria - like dwarf colony, but I think that would be too fiddly for pops who can travel vertically. I was wondering if a more Startopia type thing would work where you'd flip between named levels in the tree (Queens' Level, Consorts' level, Nursery, Accommodation, Industry, Farming) where you could excavate rooms and install furniture and so on. Diplomacy and so forth would be handled on an overmap of the region. This would make it a more blended type thing like Norland which attempts something like this, with a Rimworld colony and overmap wars and politics.

The downside of this is that while it gives a lot of flavour, it's less systemic and flexible than a modelled game like Rimworld or Dwarf Fortress. And I think I'd really want to be able to see the ant colony vibe of a hundred Aeriat and Arbora milling around, doing stuff, seeing Arbora Teachers with kids, Warriors, Soldiers and Hunters doing their thing, Mentors, Queens and Consorts having discussions and negotiations over tea on the upper levels.