After having tried a bunch of different things including trying to adapt this reply to my use case (I want the analyses of my apps to include the util/common libs), I’ve come to the conclusion that there is no solution for my problem.
It seems that once the task is configured, there is no coming back. In a multi-module project the only way of doing that is in the project root, and there is no way to use command line parameters to skip a module (I tried overriding the sonar.modules and doing :<app>.sonar.skip=true, but to no avail…)
But if someone does know of a way to do this (@ devs it would be nice to have) I’m interested.
Looking at the bright side of things I found a way to get to something that kind of works by setting within sonarcloud’s Administration >General Settings> Analysis Scope patterns to not take into account the other app.