It was Alex who told me in chat once, and then I adjusted my Substance Painter export preset to take this into consideration.
So I have two export presets now. One for TGA export for rapid adjustments and fixes when I use the model viewer without having to convert to DDS - this does not swap the red and green channels in the normal map.
The other export preset will also export TGA, but with red and green channels swapped in the normal map, and then I bring it all in Photoshop to convert to DDS