What I read in that article, was that there is no effect, putting the capacitor after the power supply
No, that's not what it said. It said another way was better. And I'm not sure I believe it, either, depending on the length of traces involved. For the capacitor to be valueless, the trace length between the pin and the capacitors would have to be longer than the length to the actual power source (not the vias.) And the SAM3X is not an AKM converter, anyway.