It seems the server has a parameter for specifying the packageConfig you want to analyze with: https://htmlpreview.github.io/?https://github.com/dart-lang/sdk/blob/master/pkg/analysis_server/doc/api.html#request_analysis.setAnalysisRoots (the argument packageRoots).

But I cannot make it work, and when I look at the code handling it, that parameter is never read: https://github.com/dart-lang/sdk/blob/master/pkg/analysis_server/lib/src/domain_analysis.dart#L322

Context: this is an alternative approach to solve my problem from #44322 .
Driving the analysis-server would even be preferable to running dartanalyzer.