Yes, both versions (version 2.1 and 3.0) can be run on one server.
The Windows service that runs the new server has a different name than the previous one. All you have to take care of is that you have different ports.
The old and the new Mail & Deploy version cannot run on the same port.
We highly recommend to firstly install the new release to a test environment and then roll it out as soon as the final release is ready for production.