If we considering city building games as RTS then its would be TheoTown (pc version). Its also has mods and multiplayer

Command and Conquer, any up to RA3

Cozy + RTS feels incompatible considering the entire genre is known for being constant pressure. But:

• Creeper World only requires setting up an initial defensive position, and everything else after can be done at a leisurely pace. (Might have changed with CW4, because some maps may have threat-increasing stacks, and because the creep can splash over some fortifications.
• Dungeon Keeper, which has more focus on building a lair rather than dealing with constant enemy attacks.

Cozy since you can probably let these games run for a bit without having to worry about getting your progress lost.