I'm very positive that they have updated the current server files to solve some of these issues, the client is extremely close to vanilla - it seems that their focus was on getting the basic features functional rather than having the customization of other full fledged private servers.
There are a few differences with the client, but nothing that seems to be completely related to the major issues mentioned earlier:
-modified CrashReporter.dll, crash dumps seem to go into the VindictusUS directory instead of the official server directory, probably as a way to prevent people from accidentally sending the crash dumps here back to Nexon through the bug reporter executable
-added icudb56.dll, like Tanna said this dll that hooks to the game process changes the game window name but I believe it serves as a redirector. They do not use hosts file, and the EndPoint in the db was pointed to Garena.
-added patcher.exe for game patches, PatcherPatch.exe (a patcher to patch the patcher), launcher.exe to allow the player to login and receive a proper token
-modified NMService.exe, they have removed a few IP addresses and put their own in
-modified vindictus.exe, although there doesn't seem to be anything major in here.
If you kill the NMService, you can still log on just fine and are still able to launch boats - friends list will stop working but its not too important.
You can also kill the threads of icudb56 after it is hooked on to the main process and notice that the boats still work fine.