The “buildscript” configuration section is for gradle itself (i.e. changes to how gradle is able to perform the build). So this section will usually include the Android Gradle plugin.
The “allprojects” section is for the modules being built by Gradle.
Oftentimes the repository section is the same for both, since both will get their dependencies from jcenter usually (or maybe maven central). But the “dependencies” section will be different.
Usually the “dependencies” section for “allprojects” is empty since the dependencies for each module are unique and will be in the “build.gradle” file within each of the modules. However, if all of the modules shared the same dependencies then they could be listed here.