Hi, I've scoured the internet for photos and all the throttle bodies are oriented 90 degrees from mine. I took it off to do supercharger maintenance (among other things). Should I put it back the way it was or does it even matter? 06 MINI Cooper S

 

As long as everything seals and connects properly, the orientation doesn't matter.

 

I'd install it correctly just encase... the throttle blade angle change might alter the inlet air path and decrease port velocity into further away intake runners. . I'd install it correctly juuuuuuuust encase. Imo , better safe than sorry...
it might have absolutely no change but they were oriented the way they were for a reason. So I'd just put it back how it should be. Exp so you don't run into clearance issues later on doing something else. You actually SHOULD have a bracket on the left of the throttlebody holding it down and onto the boost tube , that bracket wouldn't have allowed for it to be installed incorrectly. And that bracket actually is useful because it helps support the throttlebody and intake so it doesn't put so much pressure onto the seal where the boost tube mates to the supercharger. Because they tend to break off their mounting tab on the boost tube and leak..
imo , I'd actually reinstall that bracket AND reinstall the throttlebody correctly.