I was hoping someone would have given an experienced answer by now, but since nobody has yet, I'll offer an idea to consider: Try the HDN card in the 3rd slot and test. If all is well, great. If its not, could you move the graphics card to slots 3/4 so the HDN card can go into slot 2 as recommended?
Another option if slot 3 just won't work: move the HDN card to a thunderbolt chassis(not the cheapest option, but maybe one that would work)
