I cannot reproduce this problem in 3.0. If I have the Groovy plugin applied and if groovy source files are present, <sourceFolder url="file://$MODULE_DIR$/src/main/groovy" isTestSource="false"/> is added.
I only noticed the that the Groovy source folder is not added if there are no groovy source file yet. However, the same behaviour already existed in 2.14.
I tested it out with a new project and didn’t have the issue, and then realized that we were applying the java plugin before the groovy one in the subprojects block of the root project.
We were probably getting lucky with undefined behavior before.