There seems to be a misunderstanding between email 1 and 3 and what Mark suggested.
You should consider the mapping table 'off-limits' or invisible to the developer. The mapping table is private to POG and is used by POG to manage the relationships between 2 siblings, i.e. there is currently no way for POG to automatically add and manage columns to the mapping table. Now, you are free to alter the tables and mapping classes manually but we would not recommend it as any time you regenerate a class, your tables will not be in line with your classes.
Now, I understand that you both want to be able to add a "property" or column to the mapping object. I think if you want to do this the "POG way", you should create the 3rd property into its own object, either as a child or sibling. Example:
Exam is sibling of Student and vice-versa. Now, instead of trying to add Marks as a third 'column', you can think of Mark as actually a child of Student (i.e. a student can have many marks, but each mark belongs to only one student).
The relationship between Exam, Student and Mark will be proper and no data will be lost.
Thoughts?