It depends on where the applications come from.
If they are from most System V variants (IRIX for instance) the directory was /etc/init.d. and /etc/rc<n>.d Some used /etc/rc.d, some used /etc/rc.d/rc(n).d (Slackware uses this).
Historically this goes back to before it was standardized, so places took a description and implemented it differently.
This was "unified" by making symbolic links to make all variations work/look (nearly) the same.
In all standard cases, the links/files in rc(n).d are the ones executed for the level - the order of startup was alphabetical, so S00 would always be done before S01. And the two digit nn was the default. It worked just as well with Saa starting after S99...