No, both ways are not doing the same.
The first one does a local install on the system, usually it gets put into /usr/local while the second one builds a package and installs it with the package management system of your os, in your case this should be rpm. Usually in the second case it should be installed under /usr. The package management system takes care of all dependencies and conflicts that may arise.
On your development machine usually all the dependencies are resolved and you just use make install, its faster and has less overhead than using rpm. You build a package if you want to install it on a different machine, basically this is setup.exe on linux.
Now your build times are pretty insane, maybe dont compile on a toaster
. Beside that, i dont know how these two build ways interact with each other, maybe switching between both always requires a full rebuild. Just do a regular build, after the initial build the following ones should be incremental and much faster. Oh and you do bootstrap and configure only once. Maybe you need to run configure again after you added or removed files, but not if you just made changes.
About debugging, run the program and see if it works? Use command line options to enable extra debug options? Check the configure script if it offers parameters to make a debug build?
