Firstly, lets reaffirm the fact that US exists as an AU [for those ignorant of such terms that stands as Alternate Universe] outside of the main Naruto Storyline, to what degree is never clearly established, I've always run with the assumption that the key events surrounding Hogoromo and Kaguya Ōtsutsuki still happened but their relevance to present events ends with the establishing of chakra, the creation of Ninshuu and Ninjutsu, beyond that there's too much subjectivity and too many unknowns about their background to safely establish it.

It's safe to assume that villages were formed by the groups of clans banding together and what have you, but beyond that each village has an established history that I guarantee you most people don't take into consideration when writing their character background and further I doubt most moderators remember to make comparisons between the two. I wont say that US does not need some form of global back story in terms of where it differs from established events, but the general consensus is an assumed version of how the Naruto Universe would have played out if you essentially removed all Canon Characters. Kinzou Watagari brought an end to the Namigakure conflict and became the first Mizukage while officially formed Kirigakure, Daichu Kumogakure (strong name props to whoever wrote that) joined a small settlement in the lightning country and eventually usurped the leader and became the Shodai Raikage and Konohagakure's history is simply written as the ending of warring clans with Yuigon becoming the first Hokage (mind you I just took a brief dip in the history topics so my details may not be 100 percent), but regardless the histories are there and if you dont know where to look, I doubt any new members actually look at them and further, they could probably all [with the exception of Kirigakure] use a fair bit of updating.

Continuing with the concept of an AU, in the Manga all the clans have a standard basis [namely being Konoha as it exists as a focal point in the story line]. Where the Alternate Universe comes into play is that these clans although the initial focal point for the gathering of Shinobi in the pre-village era, are not written to be localized anywhere, specifically in the location section of the template. This of course means that anyone can make a clan member from any village without being bound to a specific village. Largely the clans themselves lack a US Canon [note a difference from actual Canon] history, now there's a strong chance this is mostly because of general staff laziness, but more to the point it's just a bit of arbitrary detail really. However, because they lack history and are widely available in any of the Shinobi Nations it is safe to assume, much like Chris established that there are branches of each clan within each village because there is no US Canon established home for these clans. As far as I am aware by US dictation none of the Canon clans are dictated to one specific village therefor whilst they may still be of the same family they are free to live in any location without stipulation.


With that being said, there is no reason to assume that by US Canon a clan spreading could not happen by natural occurrence because these clans were around long before the villages were established and [u]before[u] they became 'military establishments' and most importantly not every clan member of every clan gains access to their clan abilities and further, not every one becomes a Shinobi. There's no real reason to establish a need to explain the variance of clan Shinobi given the status as an AU and the lack of dictated clan origins.

Further, although they may be military instillation, one can not assume that the government of each village will act as it did in canon.