It seems the choice of which way to cartop the AI depends on the characteristics of one's car - I can't slide my AI straight up onto saddles, like Stringy, because the rails on my Forester require the rear roofrack to be too far forward. On the other hand, I don't have a problem with the aka braces scratching the roof, like Pirate does - presumably the clearance of my racks is a bit higher.
Chris my Thule roof racks are very adedequate to carry the AI inverted once up there. I like others here however found the AI is very unbalanced in the inverted position and impossible to get up there one up without risking significant damage to the car. I found that the only practical way I could carry the AI inverted on the roof racks was to put it up there right way up then flip it over. This involves an extra step when both loading and unloading and can be a bit of a hazardous process in high wind situations. Also far less salt water dumps onto the car if I carry it upright, almost nothing if I wipe the hull first with a towel before lifting it up unlike when inverted when it drips from all the nooks and crannies as well as the wet seat. I have read and viewed pictures here of several methods of loading and transporting the AI on the racks some quite elaborate and expensive but IMHO the system I am using is simple and cheap and fits the bill perfectly....Pirate