Not 100% certain about the back to back connections supporting either PPP and HDLC but believe they can.
With different interfaces, you should be able to use them with different protocols. Depending on the protocol, you can sometimes run different process instances of it. If VRF is supported on your routers, you can also run multiple instances of the same protocol.
Running multiple, or instances of, protocols on the same router allows you to work with some of the most "interesting" routing considerations.