tokenValues hook is called incorrectly, resulting in unpredictable values/emails not sending

The definition of hook_civicrm_tokenValues specifies that the $values argument is an "array of values, keyed by contact id".

E.g.:

$values = [
  123 => [
    'contact_id' => '123',
    'first_name' => 'Jon',
  ]
];

However, api/v3/Email/Send.php sends the $values as a single-dimension array:

$values = [
  'contact_id' => '123',
  'first_name' => 'Jon',
];

This leads to unpredictable results. In at least one of my extension's cases, it changes the value of preferred_communication_method to a value that's not HTML, Text, or Both, which leads to the email not sending at all.

It looks like the code @mattwire wrote in !3 (merged) to use TokenProcessor doesn't avoid this formatting issue either.