Overrides through extends — https://github.com/babel/babel/pull/7091#issuecomment-357444478

.babelrc

{
  plugins: [
    ['./plugin', {label: 'plugin'}],
    ['./plugin', {label: 'plugin'}, 'named']
  ],
  overrides: [
    {
      test: 'foo.js',
      extends: './extends.json5',
      plugins: [
        ['./plugin', {label: 'override'}, 'named']
      ],
    }
  ]
}

.gitignore

node_modules

bar.js

// npx babel bar.js
[]

extends.json5

{
  plugins: [
    ['./plugin', {label: 'extends'}],
    ['./plugin', {label: 'extends'}, 'named']
  ],
  overrides: [
    {
      test: 'foo.js',
      plugins: [
        ['./plugin', {label: 'extends.override'}, 'named']
      ],
    }
  ]
}

foo.js

// npx babel foo.js
[]

package.json

{
  "name": "fdf830ce929a8641651f7838ea4efab1",
  "version": "1.0.0",
  "description": "",
  "main": "foo.js",
  "scripts": {
    "test": "echo \"Error: no test specified\" && exit 1"
  },
  "repository": {
    "type": "git",
    "url": "git+https://gist.github.com/fdf830ce929a8641651f7838ea4efab1.git"
  },
  "keywords": [],
  "author": "",
  "license": "ISC",
  "bugs": {
    "url": "https://gist.github.com/fdf830ce929a8641651f7838ea4efab1"
  },
  "homepage": "https://gist.github.com/fdf830ce929a8641651f7838ea4efab1",
  "devDependencies": {
    "@babel/cli": "^7.0.0-beta.37",
    "@babel/core": "^7.0.0-beta.37"
  }
}

plugin.js

module.exports = babel => {
  return {
    visitor: {
      ArrayExpression (path, state) {
        const node = path.node
        node.elements.push(babel.types.stringLiteral(state.opts.label))
      }
    }
  }
}