ยง27.9 in the Documentation shows off a lot of the options you can use for having extensions interact with other extensions.
Notably for your case, you have the ability to make certain parts of the extension used only if another extension is included via a parenthetical after a heading:
Book 3 (for use with Basic Screen Effects by Emily Short)
This will make all of Book 3 (which may include Feature A) only be acknowledged if Basic Screen Effects is included. You can also cause the reverse effect by turning the "with" into a "without". If your added feature is deeply intwined in one of the extension's general rules, you can still use the parenthetical to get into that rule through tricks such as, say, defining a truth state differently within Book 3.
Using this, you can allow the author to not include Extension C if they don't need feature A or not include Extension D if they don't need Feature B. Whether this is a better idea than making a side extension is a matter of taste and your specific extension.