Efficient Map-Making for Strategy Games

I want to make a turn-based strategy game like the Risk and Total War. I am unsure on how to handle factions and collisions.

1) I could have a different color set up for each faction and map the RGB values to faction names. So each mouse click could fetch an RGB value and find out which country was being clicked.

So this is actually a decent approach, but I wanted my game to span the entire world like DEFCON and Plague Inc. To have separate colors for each and every country in the world would make the map look ugly. I could either scale down the map or really give each country a different color and see the outcome.

2) I could set up colliders for each faction. Obviously this takes more work than setting up individual colors but I think it also allows me making the map more unique.

These are the only methods I am aware of. How could I go about this problem? If you think making a DEFCON or entire-world Crusader Kings type of game with Unity would be difficult, please do tell. I am considering scaling down the map to sort of look like Europa Barbarorum of Rome Total War.

It depends on the level of accuracy. If one wants to have accurate selection, pixel fetch approach works but is the least flexible and slow. Collision based approach offers better flexibility and if speed is a concern, you can tweak the Colliders sacrificing a bit of accuracy.
Other approaches could involve a) multiple level of details for collision geometry and then narrowing selection down from the lowest LOD to highest LOD if it involves huge map etc…

Would placing down a ton of colliders be slower than having the pixel fetch method? Also I couldn’t understand narrowing selection according to LOD.

No, colliders will be faster. Either using a MeshCollider for each country/region or using a bunch of different basic colliders will most likely be faster than doing a pixel color lookup - and more flexible.