This author reaches pretty far. The NSA paid Microsoft to acquire Skype? You can't just materialize multiple billions of dollars on a public company's income statement.
You can indeed. The figures are very large and you cannot view item level detail in the financials, only general concepts. The NSA may be propping up the Azure division or one of countless others through backroom deals over this type of thing.
In addition to selling extra-high priced items to NSA/Military/Government, the Government could allow the company tax breaks it wouldn't get otherwise.
Tax rules for a company of the size of Microsoft are not simple. It's not impossible to hide stuff.
Doesn't seem that hard. It could show up as "department of agriculture/energy/..." bought X million licenses of windows and office spread out over years, a few friendly countries, a few front corporations...