> 'the a is silent' isn't really right, because it's just a modern rendering of æ, there is no 'a' (or 'e') really.
I don't understand what you're saying. Æ is a medieval innovation, a fancier way of writing the separate letters AE when they occur in sequence. It doesn't differ from a more modern fi ligature in that regard.
(It is a letter in its own right in Old English, but not here.)
> Secondly, æ pronunciation differs depending on etymology (here, Latin's borrowing from Greek).
And this doesn't look right either. Latin has AE where Greek has AI because that is how that vowel (the PRICE vowel in English) was spelled in Latin. Whether the word was borrowed into Latin from Greek or native to Latin makes no difference to the pronunciation.
As I mentioned above, Old English Æ is a different thing with a different pronunciation, but that's not really relevant here because Old English Æ never survives with the modern spelling AE. Compare þæt -> that / æfter -> after / æsc -> ash ......
What would be an example of the pronunciation of AE differing according to the etymology of the words?