There is a way around it......
Only add the information in your mod xml that is changed from vanilla..
So in effect, if you ONLY change 1 line (or however many it is) in a fireball_spell.xml, you can just make a new fireball_spell.xml and add nothing but that one line, then that line will replace the vanilla line in that file, but the entire spell stats and such will be loaded from the vanilla file.
This works with some xml files, maybe not all. Give it a try!
It works for the coreraces xml at least, this is how i easily change the vanilla faction race colors & environment type without ever having to update it as patches and changes gets released for those races, example:
CoreRaceChanges.xml (note its not even named the same as the vanilla xml, still works)
<RaceConfig InternalName="KingdomOfGilden">
<BuildingPrimaryColor>255,194,130</BuildingPrimaryColor>
<BuildingSecondaryColor>138,95,54</BuildingSecondaryColor>
<EnvironmentTerrainType>3</EnvironmentTerrainType>
</RaceConfig>
<RaceConfig InternalName="KingdomOfPariden">
<BuildingPrimaryColor>255,194,130</BuildingPrimaryColor>
<BuildingSecondaryColor>138,95,54</BuildingSecondaryColor>
<EnvironmentTerrainType>4</EnvironmentTerrainType>
</RaceConfig>