Android Runtime doesn't play nice with productFlavors

Environment

• CLI: 6.5.0
• Cross-platform modules: 6.5.1
• Android Runtime: 6.5.0

Describe the bug
When adding productFlavors to your build.gradle, something odd seems to happen in the metadata generation and some classes aren't available to NativeScript anymore.

To Reproduce

• Create a sample project where you call console.log(com.tns.NativeScriptApplication.getInstance()); from Typescript
• Test the app, it should work and return the application instance
• Now add productFlavors (they don't even have to include any specific settings) to your project, like this:

android {
  defaultConfig {
    minSdkVersion 17
    generatedDensities = []
  }

  flavorDimensions "api"

  productFlavors {
    minApi21 {
      dimension "api"
      versionNameSuffix "-minApi21"
    }

    minApi17 {
      dimension "api"
      versionNameSuffix "-minApi17"
    }
  }

  aaptOptions {
    additionalParameters "--no-version-vectors"
  }
}

android.variantFilter { variant ->
    // Don't build minApi21 apk for debug.
    if(variant.buildType.name.endsWith('debug') && variant.name.contains("minApi21")) {
        variant.setIgnore(true);
    }
}

• Remove your platforms folder
• Run the app again, now the com.tns.NativeScriptApplication.getInstance() will result in a Cannot read property 'getInstance' of undefined error.

Expected behavior
Behavior should be the same as without productFlavors.

Sample project
https://github.com/jerbob92/nativescript-productflavor-bug