I wonder if it was awkward in the studio when they were working on the Hearthfire DLC for Skyrim, and someone came out with their own "build your own home" mod before them.
Granted, Bethesda started on that concept internally only a week after Skyrim's release and revealed it with their game jam sizzle reel after that mod came out, and offered plenty of stuff it didn't (like hiring stewards and adopting your children, resplendent with voice acting), and "build your own house" isn't a difficult idea to think of.
As for what they should adopt for Fallout 4 from mods? Well, a ton of the most popular mods for Skyrim were about having more interactivity with the atmosphere itself; the NPCs reacting to the weather in Wet & Cold, and weather having a significant effect on you in Frostfall. I'd hope anything they do isn't as heavy-handed as Frostfall, though; that mod will heavily shift the focus of the game to survival unless you trim down most of its features.
Specifically for Fallout, I really hope if the Repair system is still anything like it was in 3 or NV that they'd incorporate some ideas from some of the repair overhauls in those games. Weapon overheating and Companions Command & Control are also both really good mods they could take a hint from.