Insofar as we do not physically have the Qur'anic manuscript compiled by Imam 'Ali, it is not possible to answer this question with the certainty that comes from seeing things with one's own eyes. Rather, it is necessary to rely on historical reports, and the validity of historical reports can be debated.
Anyway, one difference is that it is reported that Imam 'Ali added commentary and explanations to the codex that he compiled, including an explanation of when/why the ayat were revealed (asbab al-nuzul) and also a broader explanation of the ayat.
It is also reported that Imam 'Ali's manuscript was arranged chronologically, in order of the date of revelation, whereas the 'Uthmanic codex is not arranged chronologically.
In any case, we have been told by the Imams to use the codex that we have today as it is, so it is good to have faith that this is what we are meant to be using.
Our leading scholars do not accept the claims of abrogation of many verses in Quran except one verse which is in Sura al-Mujadalah , verse 12 ( O you who believe: Give a charity ( Sadaqa) when you consult the messenger in secret) before doing that) Sura 58, verse 12.
'This verse is the only verse in Quran which was abrogated because no one from all Muslims emplimented it except Ali Ibn Abi Talib (AS).
Other verses which have been claimed by many as abrogated are not really abrogated. More details are in Tafseer al-Bayan by Sayyed al-Khoei.
The Qur'an was compiled in chronological order by Imam Ali (AS) as we read in our books. Qur'an was also compiled in the present order by Imam Ali (AS) according to the orders of the Prophet (SAWA). The Prophet (SAWA) used to order Imam Ali (AS) to put every new verse in the place where the Prophet used to order, so it was not according to chronology but the wisdom and the aim of guiding people to the Truth.
Wassalam
Books on Islam, Muslims, Prophet Muhammad(s), Ahlul Bayt.
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