My logic is, clean the water before it hits the refugium and back to the tank... I would put the skimmer first, any reactors, and the fuge at the very end before it shoots up the return... just my two cents.
Triton method adopts the fuge before skimmer method. So the fuge first method is definitely being implemented. I think the idea is that this allows the fuge to do the majority of the filtration and the skimmer serves as secondary.