Answer: Yes.

Actually it is personal preference since some riders want to avoid the headtube paint damage which can occur if the housing stops are located fairly low on the downtube where downtube shifters bosses are installed. If the cable stops are on the head tube or high on the downtube, as with many newer frames, paint abrasion by the housing is a non-issue.

Depending on the frame and cable stop locations, it either has no effect on the shifting or can have a deliterious effect.

And no, I don't think Specialized set the bike up that way initially.