The "ae" example was used as an introductory example for us English readers. Unlike the Arabic examples where ligatures are mandatory and supported by most Arabic fonts, not many English fonts have an "ae" ligature these days. Not to mention this is a web page and a user can freely apply their !important font styles.
Using æ to mean "treat it as an 'ae' rendered by ligature which is visually indistinguishable" does not mean the author knows nothing about this (although the wording can use some improvement to reduce the ambiguity).