no, the air bubble wont make much of a difference on this particular silverstone cooler. the air bubble is most problematic when the pump is on the top. the pump in this cooler happens to be in the rad so you are good. you will still get an air bubble on the cpu which will create a minor hotspot, but effect will be minimal - i think. probably you'll just see one of your ccds running hotter than the rest over time.

however, in your case i would have still personally gone for an air cooler to keep the bottom intake completely unimpeded by a radiator. no real need for an aio when using blower cards, since they throw heat outside the case, away from cpu. look into the arctic freezer 4u-m if you like, excellent quiet and cheap air cooler for str5.