I am so glad you brought up this example. (Example 9.1-1 acyl-S-CoA on page 121 of the Chemistry Codebook.) This is the first example in Section 9 which discusses abbreviations and acronyms. When examples are taken out of context, unless you are familiar with the topic it is sometimes hard to know exactly what you are looking at. In this case, the letter S is not representing the element sulfur. It is an abbreviation (something to do with left hand/right hand orientation in organic molecules, within the subject of stereochemistry) and so --as an abbreviation-- it carries the English letter indicator because it is a single letter. You are correct that *if it represented sulfur, there would be no ELI.
The elements in the Periodic Table are *not abbreviations. They are chemical symbols. When following the Chemistry code, do not use ELIs with chemical symbols, in any context (narrative, structure, table).
The trick here is to know whether the letter is an abbreviation or an element. In the context of a textbook, you will probably know. If you don't understand the material, find someone --a chemist, a chemistry teacher-- who can tell you what you are looking at. Sometimes the internet can help, too.
I send greetings to la Belle Province!