Excellent question...and I wish we could have an equally good answer to it.
I would be quite qualified to answer this question since I was a pearl farmer for the last...30 years? Seems like yesterday!
It all boils down to the "Pearl sac". As you know, the "pearl sac" is a sac-like group of cells that originated in -or from- the mantle's epithelial cells (those that are in direct contact with the shell). If the pearl sac has "errors", these will translate unto the pearl as flaws.
What are these errors? Unfortunately, very few people (only one, to my knowledge) have been able to "follow" the development of the pearl sac in its initial phase after pearl surgery, and at that time the technology was inadequate. At best, we can only surmise what really happens with the pearl sac. so, these errors are cause by a group of cells that might develop a malformation or just have a hormonal imbalance (hormones are essential for pearl production) and depending on the type of mantle cell errors we have is the type of flaw you will end up.
I don´t remember a source for information...since I don´t work at the Cortez Pearl farm I no longer have access to a large amount of books and articles I had. But let me look into my library and see what I can find about this subject.