As told in my previous post, the method proposed by Gareth and used in your boost_campus theme is exactly what I had done.
I had not check improvements in local_boostnavigation for a while (since I had local implementation to fit our needs) and was not aware of the possibility to add custom root nodes, which is a feature I was missing. I think the only thing still missing for me is the possibility to choose the position of each custom node. (for instance, my authorities demand that a link to an administrative tool dedicated to students appear just below the dashboard node).
Anyway your work is brilliant and inspiring