I mentioned earlier the possibility of choosing an install prefix like /usr/local/samba, which installs the Samba libraries in a directory that may not commonly exist on distribution-managed machines. One possible effect of this is that you may turn up bugs in configuration and compilation scripts of other packages.
A configure script for another package may accept arguments related to the location of Samba libraries and header files, but compiling the package with these options set might not work. This isn't very surprising, it's a compilation option that is probably rarely used, so bit rot has a tendency to set in. A change somewhere that accidentally breaks the compilation when Samba is installed in an unusual place might not be noticed for some time. By putting Samba in its own directory, you are setting yourself up to test a valid, but rarely exercised option. You may find yourself submitting bug reports and patches to the package maintainers.
As I've said before, maintaining your box without a package manager and distribution is not easy. It's quite a bit more work, but it does force you to understand more about how the system is set up and what it's doing. For people who like the extra control and understanding this provides, this is a useful technique.