If 2 (or more) mods changes settings in same game-file (and uses different way of coding), those 2 mods are not compatible, and can't be used in same play-trough. So we, as mod-users, must be aware and if conflict, make a choice.
And for none-experienced mod-users, this can be annoying and difficult to understand.
And of course; this imply that we have a easy way to "see" a conflict.
Example:
Merge manager complete, with 2 unresolved conflicts:
1) Mod A and Mod B need manual merge, due to make sure what priority should apply.
2) Mod A and Mod C changes the same value, on the same object "Original game has Starting Warrior = 1, Mod A has Starting Warrior = 2 and Mod C has Starting Warrior has Starting Warrior = 4. Make a choice."