According to the phpbb developer wiki it is possible to write authentication plugins that use a custom user_id instead of the default sequence.

I did write an authentication plugin that uses an external id as user_id and removed the sequence from the user_id column in the phpbb_users table.
Here the code I use to generate a user_row returned by the login function of my authentication plugin upon successful authentication:

	$new_user_row = array(

		'user_id'	=> $external_user['loginid'],

		'username'	=> $external_user['username'],

		'user_password'	=> phpbb_hash($password),

		'user_email'	=> $external_user['email'],

		'group_id'		=> (int) $row['group_id'],

		'user_type'	=> USER_NORMAL,

		'user_ip'	=> $user->ip,

	);

And indeed user profiles can be created using a custom user_id, but
unfortunately the group is not set correctly.

When looking into the phpbb_user_group table I realized that all new entries did look like the following rows:

As you can see the user_id column was always 0.

This pointed me to look into the add_user function to find the error.
It turns out that the add_user function ignores the user_id field in $user_row when adding the entry to the USER_GROUP_TABLE.
Instead it was using $db->sql_nextid() as user_id value, which is obviously fine when using the generated user_ids, but when using external ids breaks the link between user and group.
Here the questionable snippet from the add_user function:

$user_id = $db->sql_nextid();

// Insert Custom Profile Fields

if ($cp_data !== false && sizeof($cp_data))

{

	$cp_data['user_id'] = (int) $user_id;

	if (!class_exists('custom_profile'))

	{

		include_once($phpbb_root_path . 'includes/functions_profile_fields.' . $phpEx);

	}

	$sql = 'INSERT INTO ' . PROFILE_FIELDS_DATA_TABLE . ' ' .

		$db->sql_build_array('INSERT', custom_profile::build_insert_sql_array($cp_data));

		$db->sql_query($sql);

}

// Place into appropriate group...

$sql = 'INSERT INTO ' . USER_GROUP_TABLE . ' ' . $db->sql_build_array('INSERT', array(

	'user_id'		=> (int) $user_id,

	'group_id'		=> (int) $user_row['group_id'],

	'user_pending'	=> 0)

);

$db->sql_query($sql);