The current implementation of building skins is pretty rigid: all or nothing
Your base will be the same skin if you use the auto-upgrade feature, there is no way to mix and match building skins unless you spend a severe amount of time upgrading in the right order: wood skins first, stone skins etc...
https://codefling.com/plugins/building-skins
This would enable players to mix and match building skins for their base, this potentially could lead to some very beautiful builds! And also it can break the "monochromatic" look of bases made with autoupgrade with the skin. And it could be added to both Survival and Scourge servers