In order to avoid a modx finger print, I integrated the root config.core.php into the index.php (plus renaming and moving around the root directories). Probably, I can achieve the same goal with .htaccess rewriting.
Technically, I'm free to put the assets directory anywhere. The “hardening MODX” documentation even suggests moving it to another server — possibly without PHP.
The manager and connectors directories are somehow self-contained: both have a separate config.core.php, can be moved to arbitrary directories/URLs. Assets isn't and extras rely on a config.core.php in “assets/..“.