It was a bug, and probably that option has never been available in the customizer. It was an issue with the internal setting name. The customizer breaks when you use the same internal name for more than one setting, and does not display any of the duplicates. I think the name for the option, plus the name for the custom CSS have been the same for a long time, and thus neither would have been displayed.
The fix will show up in the near future, but doesn’t seem urgent enough even to post a bleeding edge fix since the option is available in the legacy options.