Perl based product company, that also uses a Perl based product for CMS (WebGUI) and other things.
So, yes I completely understand... we are working a way to make a "Perl Runtime Engine" type of thing to get it out of the hands of the OS to screw it up.
Effectively making a /something/prereqs/{bin|lib|libexec|etc|wth} for "essential runtime" things including MySQL, Perl, Apache, amoung other things.
/something/{appname}/{bin|lib|etc} for the specific applications and data stores...
But again, from a non-dependance on the OS for anything higher than networking/storage/filesystem/(maybe authentication) functions.