You can simply do it with v.check:

const validValues = ['1', '2', '4'];

const Schema = v.object({
  // ...
  user: v.array(
    v.pipe(
      v.string(),
      v.regex(/^\d+$/, 'Invalid ID format'),
      v.check((item) => validValues.includes(item), 'ID is not allowed')
    )
  )
});