I always heard that the side mount on the fireman's side is so it isn't so loud for the engineer. Not as much of a problem for the fireman as his is often on the deck.
As for 41's whistle location, it is not clearance as all the other RGS engines and leased power had their whistles up top with no problems. Another RGS mystery. Somewhere between 1892 when she had the whistle on top and the earliest days of the RGS the mechanics decided to move it.
One thing about the short lever it takes a lot more ooomph to blow 41's whistle that it does the 340 or 346, so it isn't a question of mechanics to make it easier to blow the thing.