I think what you're missing is that packaging isn't a single self-contained process. It is a wrapper for a large number of separate processes which all need to work by their own rules, so you will be asked questions which are relevant for those processes which might not be relevant in the packaging context.
So packaging includes compiling and linking from source code. That in turn calls a configuration script, which Neal and I have just discovered might be able to influence the final content of the RPM depending on what's available on the build system (we're not quite sure about that but we've found an anomaly, and it makes a certain amount of sense because the purpose of the configuration is to adapt the compile and link process to the particular needs of the machine for which the program is built). It also includes installing the application into a dummy environment and copying the result into a series of archives to be included in packages. All these use processes available on the system but not primarily designed for packaging.
Linux is a system that uses what is already there. Very few things are self-contained. Most things are interdependent, and the questions and their default answers make sense in their originally intended context.
But your questions were sensible if packaging were a single, standalone, top-down-designed process, and it is good that you have the right sort of enquiring mind for it. Keep going and it will start to make sense. We're all learning here.
