In some sense there is a process that is something like a Windoze registry. There are module dependencies that must be satisfied within Linux. Linux is written to be somewhat modular. Going from an rpm-based package management system to a purely compiled system won't eliminate those dependencies, although it MAY hide them until execution time.
If what you are trying to compile provides the basis for modules used by other programs and that compile is somehow hosed leaving an incorrect module or no module, then that would a bad thing
. Usually in the compile/make/install process, there is a point at which no harm is done. Even if you end up installing a bad module or program, it is possible to uninstall/unmake, or at worse redoing with the previous version. Sometimes the old version is left out on your system, sometimes it is replaced. However, to discover all this you will need to read the documentation with or surrounding the software that you want to compile.