Why unifying alef matters
أ إ آ ا are one letter to a reader and four different tokens to a model. A corpus that keeps all four teaches the model to spend capacity on spelling variance instead of on language - and a search index that keeps them fails to match the same word typed on a different keyboard.
Why diacritics are not always noise
Removing tashkeel cuts the token count sharply and is right for ordinary prose. It is wrong for Qur'anic text, poetry and teaching material, where the marks carry meaning and pronunciation. That is why it is a switch and not a default.
The characters nobody can see
Direction marks and zero-width joiners survive a copy-paste out of a PDF or a chat app, then sit inside a JSONL file where no reviewer will ever spot them. They change the token count, break exact-match comparisons, and are reported here by name and count.