Why does Qsys create copies of the source files when it generates a system?

Could you kindly elaborate the first point?

As for the second one , it seems that there is workaround for it, however it would be great if we can specify the library name for the Qsys system (rather than it being same as the Qsys system name itself) and also what libraries the source files for Qsys components should be added into. There is .tcl script in the form of .qip file but this gets overwritten each time we generate the system.