Hey there.
Any setup with multiple SonarQube instances is going to get messy pretty quickly, with a different version of the main branch being analyzed and different new code periods.
What we recommend is a single, central SonarQube instance, and branch analysis (available in Developer Edition and higher) where developers can submit their own branches for analysis. This also means consistent Quality Profiles, Quality Gates, and other project settings (like inclusions/exclusions).