While I don't doubt playing on the elements of Minecraft and it's ilk will be a big part of the justification and marketing, I think it's the Fallout 3 settlement mods that were more of a direct inspiration. New Vegas did a bit of that with weapon customisation and the like. It does seem like an ancillary feature for the sandbox experience though, rather than something with story or quest significance. The focus on words like optional give it away. But people enjoy that. Hearthfire was very popular, for example.
I play a lot of mods from Nexus, and you are right. There are more features drawn from inspiration in the mod community than anything else. It's sort of a wink-nudge-nudge thing. Bethesda has a virtual team of free ideas floating around out there in the mod community that they are free to tap into and use as they see fit. It is its own dynamic and relationship. It's one of the many things that make FO an ES special; and it really broadens the fan base. There is nothing else like it at the AAA-game development level. Nexus membership and downloads have soared since Skyrim.
I noticed several things that seem to have been drawn from that free well of ideas...especially weapon customization, which we got far too little of imho.
He also said that the game is not reliant on the village building mechanic, and that you can bypass it without really missing anything, and feel free to play the game without using it. Now, to me, that is what makes Bethesda...Bethesda, and it is something that is amazing in modern gaming. Most developers spend their time trying to restrict and control players, Bethesda adds big, big content, that many players won't even experience because they don't want to bother with ancillaries.