The game must be started to install the mod into the game. Mods found in the Steam Workshop can be installed by navigating to the mod’s page and clicking Subscribe. Mods can typically be found in the Steam Workshop or various community sources.
Mods can be installed in a few different ways, depending on how the author chose to share it. If you play fallout:new vegas however, you can’t use the console AT ALL if you want the achievements. Then restart it, and reload it, and the steam achievements are enabled again.
The worst thing that could happen using mods is as Kevin mention OR getting the achievement inmedately, due to the mod automatically meeting the achievements criteria, such as giving you X item or unlocking X tech or whatever achievements are there. Modding is now officially supported in Afterbirth+, enabling users to mod the game using the Lua programming language and to upload their creations to the Steam Workshop.