So far, it does. I haven't used it for 2.5.0, but no one has complained about it yet.
As with any MODX upgrade, I'd still recommend backing up the site first, though.
BTW, the MODX .zip file doesn't contain a config.inc.php file, packages, or any of the other files you're worried about. Extracting it in the MODX root won't remove any existing files, it will just overwrite old files and add any new ones, so it shouldn't overwrite anything of yours.
In fact, unzipping the files to their correct locations is exactly what UpgradeMODX does (just a lot more conveniently).