Reply To: al-Qaeda
So sorry for the delay in responding - I didn't see the additional question posted.
I understand your rationale that it's clear that al is not being read as also-Qaeda, however that is making an assumption that the reader is familiar with the word. If this is a new word for the reader, they would have no way of knowing what is correct or not. Using the letter indicator takes away any potential doubt.
Since al is the short-form for also and short form words are used in contact with hyphens - technically the letter indicator should be used.