MikeF should have warned you that I like to compare Afghanistan (in general, not in some of the particulars) to Arizona between 1860 or so and 1876. The similarities are fascinating, including a transition from preparation for a high-intensity conflict to more Small Wars-style operations, muddled command arrangements after 1865, and a number of competing interest groups (to include a local government that profited from Indian wars, a number of different tribal groups, Federal government representatives, and the Army often caught in the middle).
As for the development of the West, the railroad was certainly an important factor, but possibly not the decisive one. It wasn't reliable or truly national for some years (the whole "Golden Spike" thing aside), and its impact was limited until the mid to late 1880s outside of its main corridors. I would contend that industrialization had a bigger impact, to include the national thirst for precious metals (something we had in common with the Spanish Empire not that long before us). Prospecting, and later deep rock mining, drove a great deal of the settlement and development in many areas of the West (miners have to eat, and they have specie to buy goods). There was also a great deal of displacement going on, even among the new Anglo arrivals.
And I don't know if you could count on insurgents ignoring a railroad. Railroads bring outside influences, modernization, and any number of assorted things they might not appreciate or welcome. Also, if it makes it easier for Government forces to concentrate it becomes a target for that reason alone.
Just some thoughts in response to your thoughts.
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