While this makes sense for a single layer scaled, I don't think it's an expected behavior for changing the layout scale.
The MouseX and MouseY should return layout coordinates scaled according to the layout, as the manual states:
Return the position of the mouse cursor in game co-ordinates. This is (0, 0) at the top left of the layout. It changes to reflect scrolling and scaling. However, if an individual layer has been scrolled, scaled or rotated, these expressions do not take that in to account - for that case, use the layer versions below.
As the manual describes, the specified layer positions MouseX(0) should be only used when a single layer has a different scaling than the others, otherwise MouseX should cover it.
So it doesn't seems to be a problem with tilemap's PositionToTile, but the MouseX and MouseY not accounting for layout scaling.
@Ashley Shouldn't it account for?