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I've managed to pin it down to this working for exclusions:

dependencies {
  someConfig('com.example:artifact:1.0') {
    exclude group: 'com.example.exclude', module: 'excludeArtifact'
  }
}

However if I first declare the dependency then add the exclusion later it does not work. For example:

dependencies {
  someConfig('com.example:artifact:1.0')
}

configurations.all {
      exclude group: 'com.example.exclude', module: 'excludeArtifact'
}

These rules are visible on the configuration itself, so in order to access them you need to call

Configuration#getExcludeRules

Thanks, I'll try that