I've used the term "breaking packages" a few times. As I said, I maintain my Linux boxes without a package manager. So, how did I get these Linux boxes?
My main Linux computer has over half a million files in its filesystem, and over 3000 separate executables. Where did they all come from? You need some way to start out, your computer isn't going to do much without a kernel, a shell, and a compiler.
In 1994, I installed Slackware on a 486-based computer. This computer had about 180 MB of hard drive space (nowadays that wouldn't even hold half of the kernel source tree) and 16 MB of RAM. At that time, Slackware didn't really have a package manager. It had packages, just compressed tar files of compiled binaries, grouped by function. If you weren't interested in networking, you didn't download the networking file. If you weren't interested in LaTeX, you didn't download that file. There were only a few dozen "packages", because of this very coarse granularity. The functions like "upgrade", "install", "find package owning file" weren't present. An upgrade was the same as an install, just install the new package into the filesystem, and it would probably replace the old package. To find out which package provided a certain file, you could look in per-package lists of files.
So, I never really had a package manager on that system. When I needed new programs, I downloaded the source code, compiled it, and installed it. When I moved to a new system, I brought backup images or a live hard drive to the new computer. I didn't start with a blank hard drive, I started with the hard drive from the old computer I was replacing. Over the years, I have replaced every executable that was installed in 1994 (I know this is the case because all of the files installed then were a.out format, and I have only ELF binaries on my computer now).
Sometimes, though, I've started with a computer that had a distribution installed on it. At a previous job, my laptop came with Mandrake Linux installed on it. I tried to keep the distribution alive for a while, but eventually got impatient with the package management system and broke the packages.
So, if you give me a new Linux computer and tell me it's mine to modify, a good first step for me is to kill the package manager. On an RPM-based system, that's generally achieved by recursively deleting the directory /var/lib/rpm. After that, the rpm command will stop working, and I have the finer control and more difficult task of managing the box myself.