I had a hunch which, when followed by a quick image search, was confirmed. Early roundhouses seemed to be set up with smokeboxes facing the turntable. By the 1910's the practice seems to have changed to tenders facing the turntable. I suspect this was not a hard and fast rule, but rather one that developed over time by infrastructure changes.
While the smokejacks above the locomotive were certainly a concern, they could be easily moved in comparison to pits. In the days of Stephenson valve gear and indeed, in general, access under the locomotives machinery was essential. Early pits were seldom the entire length of a roundhouse. Thus, if a pit was towards the turntable end of a roundhouse, it would likely be unlikely for it to change until the next renovation.
I cannot guess, however, why they were set up that way in the first place. Perhaps it had to do with rooflines or access to natural light. More research might turn something up. I think Joe's idea based on the. MEC Mountain Division makes sense.
Steve