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There seem to be two major lines of reasoning here, both conjecture, because apparently Congress never explained itself. Arizona's state historian Thomas Edwin Farish wrote:
For some reason, to this day unexplained, the greater portion of the land in this Arizona county [Pah Ute County] was ceded to the State of Nevada.
The first line of reasoning is that Congress wanted to create states with unified interests. As Beulah Hershheiser put in is his official state history of Nevada:
. . . the desired tract was a mining district; that Nevada was a mining state; and that the interests of the two were therefore identical.
Secondly, Congress may have felt comfortable rewarding Nevada with valuable resources at the expense of Arizona, as Arizona had recently sided with the Confederacy, and in fact had been granted territorial status by the Confederate government.
Source: Mark Stein, How the States Got Their Shapes Too