I would say that it's only idiomatic if the person doesn't normally sit at their workstation. Hence, in the context of an office, it's not idiomatic, but, in the context of a salon (where the hairdressers generally stand while they work), then it could be considered idiomatic.
The real question is, are there contexts where you'd use the phrase "where someone sits" if they are not generally sitting down in that location? For example:
The pickers take their baskets to the roadways, where the foreman sits with several women and a number of baskets of about a bushel capacity lined with canvas.
Does that foreman have a chair at the side of the road? If not, I may have just found the phrase used as an idiom.
That all said, if you want to ask where somebody works, then asking:
Where do you sit on the second floor?
is perfectly fine.