Incorrect call to user_pass_rehash(), 3rd parameter is not the email address

As I was looking at a website logs, I noticed some errors in Core (#2568673: user_pass_rehash() checks field "login" as a string instead of an integer) and that error led me to think that the 3rd parameter of user_pass_rehash() was the email address of the user.

Not at all, it is the "login" field which represents the timestamp of the last user login attempt. So all your calls to your function named logintoboggan_eml_rehash() are wrong. They need to specify $account->login and not $account->mail.

I would also suggest you pass $account->uid as the new 4th parameter:

function logintoboggan_eml_validate_url($account){
  $timestamp = time();
  return url("user/validate/$account->uid/$timestamp/". logintoboggan_eml_rehash($account->pass, $timestamp, $account->login, $account->uid), array('absolute' => TRUE));
}

function logintoboggan_eml_rehash($password, $timestamp, $login, $uid) {
  return user_pass_rehash($password, $timestamp, $login, $uid);
}

There are "many" locations where you call logintoboggan_eml_rehash() so you want to make sure to fix all of them.