Excellent question. I was wondering the exact same thing.
I decided to build my own internal linking system for that very reason, but, of course, that really only helps the people I link to and not me.
I think there is a reasonable chance that Google might decide to downplay the importance of links originating from LinkManager controlled pages. It would only take a few lines of code in the Google algorithm to make this happen.
Any other thoughts?
Freecloud