Fans of the post-apocalyptic RPG franchise have been eagerly waiting for the Fallout 4 mods. While some crafty users have already released some mods, those were not made with the Fallout 4 Creation Kit, which has yet to be released publicly.
However, the beta has been going on for a while (in fact, a quest mod with two new dungeons has already been released) and now some users have confirmed on Reddit that Fallout 4 mods apparently disable achievements.
When you install a mod and load a save, any saves made will be separated into a new save slot. Example, say your character's name is John. You install a mod, play around on John for a little while, and save the game. Instead of saving to the regular John section of your save menu, it will create a John [Modded] section.
If you were to, say, play around with mods for a few hours but want to go back to earning achievements, your only option is to load from your original John files, losing any progress you made with mods installed. So if you plan to play Far Harbor, for instance, and want those achievements, but also want to play with mods, you'll need to load back to before you installed any mods, and no progress you made with mods installed can be carried over.
Even if you were to uninstall all the mods on your modded character, that [modded] flag is checked permanently, and you can't earn achievements without loading to the original.
Beta testers are apparently by and large not happy about this. Bethesda staff has not commented on whether or not this is up for debate. The general consensus seems to be that mod authors don't want users to have a reason to keep mods disabled, they don't want users to be made to feel like mods are cheating, and they don't want users to have a reason to not use mods. Want to install a mod that fixes a broken quest, you can't get achievements. Want to install a mod that adds a new weapon, you can't achievements. If you want to use the Unofficial Patch, you can't get achievements. Some people argue that mods will enable players to cheese achievements, but that was NEVER EVER an issue with Fallout 3, NV, and Skyrim. Mods are content, not cheats.
As of now the current plan is presumably for this to extend to consoles for achievements/trophies as well.
While on one hand it is understandable that Bethesda would make this choice, on the other hand mods have always been vital to their games. Many gamers use them regularly and surely at least some of them won't be happy to learn that no achievements can be learned while using mods in Fallout 4.
As a reminder, Bethesda has promised a way to introduce Fallout 4 mods to consoles as well (on Xbox One first and then PlayStation 4). In the meantime, the Fallout 4 1.5 update is available in beta form on PC, adding the highly anticipated Survival mode.