One of the purposes of publishing a solution, is to refresh all modules in it, and reflect a change of an upgrade.
What I propose, is to remove unused dependencies between the defined modules in the solution.

I recommend for it to a configurable option. But it would be helpful especially in big projects, where the architecture is big and complicated.
Also, it could be a helpful option before checking the architecture in Discovery. Before the check we have all modules refreshed, and all unnecessary links broken.