With all the great mods out there + my own, its getting harder to avoid "conflicts" like this. Wish there was a better way but what i do on every new release is use WinMerge (great tool btw) to check all the new xml's against the mod directory.
Also it would be very helpful for some mods to be independent from game's files.
For example I want to alter an improvement I cannot create a simple xml file with that altered improvement only but the entire code with all improvements.
This is a common problem for modders because the updates and expansions make changes in code like the Aquatic planet mentioned here.
It would be very helpful if the game could recognize the code and I type "PlanetImprovement" in my mod and this one overrides the other "PlanetImprovement" in game's files.
Also something else, the developers could create a check in code. There is already something in the game when something is wrong you get a window reports an error on a certain xml. But it could expand to check the mods compatibility with current game version.
If someone has created his own PlanetTraitsDefs.xml game should check that the code is valid not just errors but issues like the aquatic planet.