Why? The shorter barrel is a little handier, but I can't think of any other disadvantage to a longer one. A 12.5" does have one advantage: since it uses the same pistol-length gas system, it will have a longer dwell time which should give a little bit better functioning with subs. However, most people seem to have no trouble finding subsonic loads that will cycle the 9" reliably. But the longer barrel might give you a little more margin to play with different loads, especially subs with lighter bullets.
For the OP, I'd say get the barrel you want and then see about a rail. Losing a few bucks selling the rail and buying a different one is no reason to take something less than your first choice for the rifle.
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