A method of filling pharmaceutical containers includes: filling a first plurality of containers, the first plurality of containers being supported by a first holder supported on a first step of a first transport and packaging container defining a first step height, the filling includes moving filling needles of a filling device to a filling needle height and dispensing a substance into each of the first plurality of containers; and filling a second plurality of containers, the second plurality of containers being supported by a second holder supported on a second step of a second transport and packaging container defining a second step height equal to the first step height, the filling includes moving the filling needles to the filling needle height and dispensing the substance into each of the second plurality of containers, the second plurality of containers differ from the first plurality of containers in at least one aspect.