The laws of thermodynamics will start to play out at a certain point. In theory, you won't see a significant difference in charge temps with different tank designs / orientations. The entire intercooler will remain pressurized, no matter the end tank orientation. However, if you measured charge temps at the top and the bottom, you could see a slight difference. IE: hot air rising affect. But at the end of the day, it's all about pressure drop across the core and charge temp differences before and after the intercooler. A perfect scenario would be as little pressure drop across the core as possible and as close to ambient air temps as possible. This is the challenge.
-Patrick-