The first reason, as well as the response from Microsoft, contain the real motive behind the decision; that is, Microsoft wants to make some money from this transaction. The key word is RETAIL Xbox consoles, as well as membership. With MS being the owner of the platform, I can not blame them for seeking a profit. The other two reasons invoked by the Army - and not confirmed by Microsoft - are just dust in the wind; they do not matter and I believe they don't exist (although, on second thought, there was a shortage of consoles when they first came out). Corporations live to make a profit (otherwise they would make no sense) and if you want to do business with them you have to give them at least a chance to do that. Even the Army spokesperson admitted that with their proposal there was a great chance that Microsoft would have lost on their bottom line.
Moreover, nowadays a PC with specs similar to an Xbox would probably be as expensive, if not even less so, than a console. Everybody knows bureaucracy is slow, but c'mon! This is 4 years later!