Hi @jkroeber
If you want to have the issue exclusion feature working in both SonarQube scanners and SonarLint, you should define them directly in the SonarQube UI, it should work.
SonarLint doesn’t recognize properties defined in build scripts (pom.xml, build.gradle) and this is not in our current roadmap (but I will track your feedback in our feature requests list).
Also you can vote for SonarLint read sonar-project.properties that is pretty similar.