I'm running pretty much the same setup as you, and in all the years of using CPAN and 'apt-get', they've never "interfered" with each other. I will admit that I was initially apprehensive about it as well.
With regard to your .modulebuildrc - I don't know if this is sufficient to fix your problem, but that's not how 'install_path' works; it actually takes 2 arguments, the section to install and a location to install that section (e.g., "install_path lib /home/ken/lib/perl5".) Perhaps you meant '--install_base' - which does take a single argument.
Human history becomes more and more a race between education and catastrophe. -- HG Wells