That article (accurately) points to Signal's initial funding by the Open Technology Fund, an program that gives grants to internet freedom technologies that line up with US interests and is funded by Radio Free Asia, which is under the State Department. Radio Free Asia was previously CIA-funded, many many years before the creation of the Open Technology Fund. (Also, Radio Free Asia, both in the past and in the present, is working on problems where being secure against large governments is much more useful than having back doors.) It has never been NSA-affiliated (unless you count "being part of the US government" as NSA-affiliated).

The relationship between Signal and the State Department is solely one of funding, not of technical interaction, let alone technical endorsement.