The article on the Embargo Act itself reads: "The Embargo Act of 1807 was a general Embargo that made illegal any and all exports from the United States. It was sponsored by President Thomas Jefferson and enacted by Congress. The goal was to force Britain and France to respect American rights during the Napoleonic Wars. They were engaged in a major war; the U.S. wanted to remain neutral and trade with both sides, but neither side wanted the other to have the American supplies." That's exactly in line with the thesis.
Regarding Samoa and Germany/Phillipines and Spain - this is when these policies began to change. They bubbled from the late 1800s and broke in the early 1900s.
I think there's a narrative difference here: the US broadly did not align themselves with other nations into treaties of peace and of war. The "founding fathers" specifically discussed the danger of political entanglement with other nations - the danger of allowing them to say "yes" and to say "no".
I feel like your interpretation of the Monroe Doctrine, of the Embargo Act and of Manifest Destiny are not charitable for these reasons. Of course the US was not 'isolationist'. I termed it 'non-interventionist'. Even that is not a good term, but what was meant I think is clear.
Yes the US engaged in colonialism and in trade. But it did not involve itself in the spirit of the top post: allowing other nations to have a "yes" or "no" say. It made declarations like the Monroe Doctrine. It did not make treaties like NATO or like TTIP. Categorically these are different in kind than what happened before the 1900s.
Part of that is due to a changing world (I say this in my top post). But the US was also under a different international political disposition.