No. I understood exactly what you meant.
My point is still the same. If the user downloads one mod that overwrites a modified file from another mod, they're in trouble. I'm sure you or I would be able to spot conflicts before they happened and figure out how to merge the code but not every user is capable of this.
By keeping the mods posted the way they are with instructions on what to modify, it keeps things clear by showing the user what has changed for the given mod. Making these downloaded files instead removes that level of detail.