Just my two cents -
The boards categories are great when posting a new thread, but when it comes to READING threads, I always use the "Show unread posts" link. This way it doesn't matter where it posted, I will at least see the subject line. From this perspective, I think it is a great idea - however, if people don't read the forums this way, it will, indeed, have a high potential to isolate users who navigate the individual areas manually.
EDIT: I also think that people who read the threads like I do may respond without noticing the area of the boards they are in, so at that point having them separate doesn't accomplish anything. I guess all I am saying is it may help some and may hinder others. In the end I would propose it is not really worth the effort.