I agree with the confusion on the vendor/kolab folder, I still don't have LDAP working properly on my test server. (Although, to be fair, I'm running it on a different server than I have ever tried before due to the new PHP requirements - my production server, soon to be replaced, is on 5.3.3.)
Regarding the Advanced prefs option, that has been around for a couple of releases now. I can't remember if there was any description of it when released or not. But it seems intuitive enough to me. Just like the 'dont_override' array, you should be able to put almost any preference param in the 'advanced_prefs' array. For example, mine is pretty minimal:
$config['advanced_prefs'] = array(
'reply_all_mode',
'standard_windows'
);