As humans, we can only be certain of two things, 1) direct experience, and 2) لا اله الا الله .
It appears that the first generation of believers produced copies of the Quran at least within decades of the messenger's death (as evidenced by radio-carbon dated manuscripts and palaeography). What did the Quran look like before this time? Was it merely oral? Was it written down? It is not known.
The first copies of the Quran were probably produced in western Arabia by teams of scribes working together (as evidenced by the different handwritings that exist within some of the same manuscripts). But what were the first copies made from, i.e. what were they copied from? It is not known for certain, however, van Putten has shown in his paper
"The Grace of God" as evidence for a written Uthmanic archetype (2019) that most or all copies of the first generation were made from a single "master copy" which he calls the "Uthmanic archetype."
It appears that scribes of the Quran made their copies directly from previous copies, i.e. they didn't make copies of the Quran based on oral dictation (as evidenced by anomalous spellings in the same surahs and ayahs). There are exceptions to this, such as Is 1414, which is a manuscript held at the Chester Beatty library in Dublin. It seems to follow a different tradition or maybe it is an innovative copy that spells words in a way that doesn't match other manuscripts before its time.
Over the centuries, one can expect that aberrations will occur in spelling, e.g. maybe a scribe will choose a spelling that matches the prevailing reading of his town, or maybe there will be an honest mistake in spelling, or maybe there will be a mistake in interpreting the text, etc etc etc. This is how errors build up.
Ultimately, we reach the early 1900s when AlAzhar University commissioned a group of scholars to produce an 'authoritative' copy of the written Quran for the reading of Hafs via Asim. However, they did not rely entirely on manuscipt evidence, instead, they relied on the works of orthography produced by classical scholars. These classical scholars did amazing work, however, they did not have access to the breadth of evidence available to us today. Naturally, the scholars of AlAzhar produced a copy of the Quran which was a mix of real historical spelling practices and innovated traditional practices. This copy is now known in secular academia as the Cairo Edition, and it is the copy that exists around the world in everyone's home.
The aim of
uuq114.org is to gather and merge every accessible manuscript of the Quran that is safely dateable to the period
before 1200 CE so that one would be in a good position to propose what the 'original' or 'first' Quran looked like.
As for the traditional narratives of Uthman burning aberrant copies of the Quran, or Hudhayfa appealing to Uthman to produce a definitive copy of the Quran, or the story of the believers who knew the Quran by heart being killed in battle etc etc, these stories surrounding the compilation of the Quran are unverifiable.
I've not read the work by Karim. As long as it is an academic work, and not a work that blindly adheres to Sunni convention, then go for it! Otherwise, I recommend the following:
(1) On the language of the Quran:
Quranic Arabic: From Its Hijazi Origins to Its Classical Reading Traditions, Marijn van Putten, 2022
(2) On the message of the Quran:
Qur'an: A Historical-Critical Introduction, Nicolai Sinai, 2018
As for Quranic orthography and Quranic readings, I have not come across any contemporary academic works that are devoted entirely to each of these fields that are worth recommending. There is a work by Shady Nasser of Harvard University
The Transmission of the Variant Readings of the Qurʾān (2012), but it leaves much to be desired. Even the work by van Putten I listed above (which does cover the readings) only superficially explores the readings, and I have observed patent errors in his work.
Sorry, long post!