The hubs on the S4 (pre-Brembo brakes) are identical to the SE hubs, except for the 58mm spigot. The hub is not a Toyota part, and I'm fairly certain the spindle isn't, either.the original Stephens setup used Toyots spindles and hubs. Those parts probably were drying up and lotus made a change as they were going away from the toyota brakes, too. With Lotus being such a small volume manufacturer, finding already prioduced hub was more cost effective than having a small run of custom hubs made.
I'm pretty sure it was just to prevent numpties from putting the wheels on wrong.