Not from my experience. If the FI car has a proper cooling system it should not be affected by weather as much. In the summer my SRT Jeep (NA) is considerably slower the the X5M (TT) and a little slower than the Cayenne Turbo and ML63 (TT). In the winter however my Jeep is faster than the Cayenne Turbo and neck and neck with an X5M.
Summer SRT Jeep runs 13.1 winter runs 12.6
Summer X5M runs 12.5 winter runs 12.45
It would be helpful to know the weather at the time of the runs and whether or not both vehicles are stock or not. Is your X5 running stock levels of boost or did you crank it up, and is anything done to the Jeep?
If you take two of the same vehicle, with one being FI while the other being NA, both producing the same BHP, both cars will lose power as ambient temperature increases. The rate that the FI vehicle loses power would be greater than the NA once the temperature crosses a certain point - perhaps a point where the intercooler can no longer cool the intake charge efficiently to maintain a given level of boost.
If you plotted this trend on a graph, the FI engine could maintain its rated power longer than the NA as air temperature increased since the FI engine can compensate for the less dense hot air by increasing boost. Once the FI engine reaches its practical limit for increased boost, its power level would make a sharp decline, crossing the graph line of the NA motor. The FI engine would "bottom out" at a lower power level than the NA motor. As for proper cooling, there is a limit to how much space the components can occupy in the engine bay so optimal cooling component size and placement is not always possible.