Hi Julien,
While I'm well aware of the fact that "as is" Loïc's PR may cause issues in some cases, it's a bit more difficult to understand that this topic received not much attention for the last year and a half and it was never really discussed with the community.
As you wrote in your first message, it is a long known limitation. And its impact is important: many types of plugins cannot be written correctly as files located at an agregator level in a multi-module context are simply ignored. However these files are central to the build (at least IMHO).
In this context, I think that porting the PR, start testing, report issues, think about them, and discuss would help specify a solution, and would help have (hopefully) quickly a first version covering 80% of common cases. This approach looks like to me a better (or at least more constructive) approach than just continue waiting for the specification SonarSource is working on (again you set your priorities, have limited resources, and I understand it, in return please just understand that other people may have different priorities.)
By the way (and to start the discussion), concerning the issue you mentionned: what about only considering files located at the root of the aggregator level directory as sources (i.e. avoid mixing the aggregator logic with non aggregator logic) ? what about using another property for aggregator level sources (and thus a different property validation) ? what about considering that aggregator level don't have test sources?
Let's discuss about small and unperfect steps toward a great feature!
Best regards,
Michel