if you want to make an application that loads into AutoCAD is has to be a .dll file.
You would create a class library project and load it.
The fact that is uses .net 4.0 doesn't matter. .
Maybe you are talking about making one compilation for both versions?
If you are, I think it is not possible because of the "extra" reference needed in 2013 version "accoremgd.dll", you will need to make two proyects instead only one.