The problem here should be obvious: not all mods are designed to make a game easier.
While this information originally came through a third-party, an image, pictured above, has since surfaced that backs the information up. From that point on, the saved game is going to be flagged as having modding enabled, which in turn will prevent achievements from being earned. An example given: If your username is John, the next time you save a game with a mod enabled, a 'John ' saved game will result. In his post, reddit user HakfDuckHalfMan notes that games in FO4 that have enabled mods are treated as completely separate from ordinary ones. As one reddit user has discovered, though, there is one major caveat to be aware of if you want to use FO4 mods: no achievements.
That latter point ties into modding, which Bethesda is happy to not just let fans dive into, but is proud to support. There are myriad reasons why a game like Fallout 4 is so good, from its sheer depth to its flexibility.