Is there a way to create multiple mds under one mds project?

Your below statement is not true.......... 

"..... you can't copy, refer, use functions from one project in another project "

you can add scripts from project A to Project B.

click project B \ script 

right mouse and existing item

then it will show dialog where you can point physical location of Project A script.

or else as tristaanogre says you can write sctipt extentions  for more information read this 

Script extentions are easy to use once written. But I don't use much since I need to do debug and modification time to time.

please read this also