No matter who you vote for, the government always gets in

From the article:
Glennon cites the example of Obama and his team being shocked and angry to discover upon taking office that the military gave them only two options for the war in Afghanistan: The United States could add more troops, or the United States could add a lot more troops. Hemmed in, Obama added 30,000 more troops.

Whilst the crux of the interview in unsurprising, the part above intrigued me.
Is the author claiming that the US military tells the US president what the military will do and that the president is utterly powerless to contest this?
I find that a little hard to believe and didn't see it directly cited in the interview.
 
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