Selection of the gradle build file name (similar to the -b option in Gradle) is vital, a least for gradle tasks execution, but preferably also for import.
When importing, I need only compile time direct dependencies. When executing, I need the full transitive and runtime (direct and transitive) dependencies. So, I use two different gradle build files, one for import and one for running.
In the meantime, I use the generic external tool configuration, but it is much less practical.