After several tries (768 is for the SKSE.ini indeed) I could only fix it by using the actual SMME files, seems no matter what my SKSE.ini is ignored, tried of course in overwrite folder, actual data folder, inside a mod made by myself containing the ini file...
Since SKSE is actually working as it should and I don't really need ClearInvalidRegistrations every single time I load a game I will keep it like that but I would like to understand why SKSE.ini gets ignored no matter where I do put it.