The 3.x rom is not a kickstart 3.9 rom. It has some modules that never came with 3.9 and even some of them are not available anywhere else. If you want I can list them for you, along with some of their differences.
Cloanto´s Amiga Forever 3.x enviroment is not AmigaOS 3.9! It is a mixture of 3.1 with some 3.9 components and some third party ones as Minuous and Cloanto themselves pointed out.
So to call the 3.x Cloanto enviroment "frankenstein" is not far fetched.
Pieces of "OS3.2" replace the remaining pieces of 3.1 that were still in the original 3.9 release and they are pretty well documented.