Well, for a multinational corporation, the sentence still makes sense and doesn’t seem gratuitous or sensationalized, as they could say they shifted $39B of UK profit to Ireland or something. It does leave a vague and perhaps intentional implication of crossing some kind of border, so they could have said “$39 billion of profit in the incorporated US”, I suppose.

Except PR citizens and corporations don't generally pay US income taxes. There are exceptions though, like if the income is from US activity. They do pay a few other federal taxes (like FICA, FUTA), but those aren't relevant to the article.

No taxation without representation.

Yes... I mention this because it's the only reason Microsoft's tax dodge works, since as Joe mentions, PR is part of the US.