The game reads the mods in the list from top to bottom with the bottom-most mods having priority over the top. They do not merge at runtime, which is why having a load order and knowing which mods conflict is important.
The whole point of Load Order is conflict resolution. Console players do not have tools such as FO4Edit for conflict detection. PC players can download FO4Edit for their conflict detection.
Some mods do not work together. These types of mods will be editing the same record. Whatever is lowest will have priority over the top. Some incompatibility will cause issues for the game or other mods in your load order.
- If two weapons mods edit the same base gun or any of its keywords, they will be incompatible.
- If a mod that disables the precombines and then rebuilds them to suit their mod to add their items or settlement to the world and another mod rebuilds the base game precombines, those two mods will be incompatible.
- If two scrap mods edit the same base game scrap lists, those two mods will be incompatible.
Incompatibility can lead to anything from system lag to CTD. In many cases it leads to CTD. Conflicts are not always apparent until crashes begin to happen.
Some mods can be used together to override changes one has made.
- Compatibility patches
- Addons - some mod authors have additional plugins for their mods that override previous changes
Rule of One
Only choose one of any type of mod to add to your load order until you've tested two of the same type together.