Yes when you get the RPAL it replaces your basic PAL, and yes you'll get a new five-year clock (you pay more do do them both separately than together).
Yes the RPAL allows you both ownership of restricted and non-restricted. Think of the restricted like an "and". The regular PAL just gets you non-restricted, but the RPAL gets you non-restricted and Restricted.
You can take both at the same time, but you can not just take the Restricted without first taking the Non-Restricted.
There is different subject matter taught in both, with the non-restricted including content like parts of a gun, the classification system, etc.
If you just took the Restricted course, you'd miss that content, because the Restricted focuses more on handguns and the extra laws of Restricted ownership.