[Admins]

Graal is only downloading files if needed, and it is doing the check by filename. Servers are sharing tons of files, making copies of them for each server wouldn't mean just more hard drive space used, it would also mean much more network traffic.
Using some prefix in the filename shouldn't be a big problem. The only problem with sharing files between servers is that some server could replace the good files with bad versions of the file. In v4 there is a way now that playerworlds can prepare packages of files needed for the server and once downloaded the client prevents downloading them from other servers (this feature is currently not enforced yet but will be soon),