A bit of history relevant to IC packages, but not necessarily to transformers.
The pin numbers for vacuum tubes were always numbered clockwise from the bottom, since the wires were connected to a socket on the opposite side of the mounting plate, and the voltages were probed from that side.
This convention persisted for DIP ICs and other semiconductors, even though they are usually visualized and probed from the top, where the pin numbering is therefore counter-clockwise.