The list of settled villages and towns in Neh 11:25-36 has perplexed many scholars. Several different interpretations have been offered. One interpretation suggests that the list of towns delineate the geographical extent of the province of Yehud in the Persian period or at least a paradigmatic vision of those boundaries. This interpretation, however, is problematic insofar as several of the towns are too distant for a properly configured Yehud, either they are too far west or too far south, and conversely, if it is paradigmatic, then the boundaries are simply not wide enough to be consistent with even the Josianic kingdom of Judah as portrayed in the biblical texts.
Janzen, CBQ 64 (2002):490-510, partially solved this problem by suggesting that the list registers the towns and villages outside Jerusalem whose residents participated in the Jerusalem temple and that as such the religious and political affiliations are not co-terminous. Though I do not necessarily accept Janzen's methods and conclusions in their totality (particularly those about the citizen-temple community modeled on Babylonian temples as well as his use of unprovenanced bullae), I do think he is correct on this one particular point.
But, this solution amplifies the problem created by the absence of several key Judahite and Benjaminite towns from this list, which Janzen does not really address in his article. Most notably, Mizpah and Gibeon are not mentioned in this list. The logical extension of Janzen's argument, though he himself does not argue it, is that the residents of the Judahite and Benjaminite towns and villages not mentioned were affiliated with another temple. Personally, I'm inclined to think that implied in the list then is the presence of a Yahwistic temple in Mizpah (see Jer 41:4-5; 1 Macc 3:46; and see/cf. Jeffrey Zorn, "Tell en-Nasbeh and the Material Culture of the Sixth Century," in Judah and the Judeans in the Neo-Babylonian Period [Winona Lake: Eisenbrauns, 2003]: 442-445). Gibeon may also have been a cultic center (see Diana Edelman, "Gibeon and the Gibeonites Revisited," in Judah and the Judeans in the Neo-Babylonian Period [Winona Lake: Eisenbrauns, 2003]: 153-167).1 If this is indeed the case, it brings into sharper relief the difficulties faced by the Jerusalem temple community in asserting its primacy in the Persian period.
Also, related to this case, the reference to Lachish and its villages would consequently inveigh against theories that a Yahwistic temple existed there as suggested by Aharoni and Widengren (though, I suppose there is no reason to believe that some residents wouldn't participate in a temple community away from their local one).
1 Though interestingly, and perhaps militating against my reading, Neh 7:25 enumerates ninety-five "sons" of Gibeon among the Golah; though, cf. par. Ezra 2:20, which reads Gibbar instead of Gibeon.