Here's an analogy: let's say you've written a command line tool and you want to install it. The simple answer is to just copy the binary to /usr/bin. Does it need config files? Library dependencies? That's fine, copy them to the appropriate directories. But then you, as the sysadmin, have the responsibility of remembering exactly what the state of the system is. If you need to make changes later on, you need to spend time figuring out exactly what needs to be updated, and then manually apply those changes without making mistakes.
The cleaner solution is to use a package manager like rpm or apt-get. You have to spend some time up front to package your code, including explicitly defining things like package dependencies and clean-up scripts. But once that's done, you can let the package manager do the work of figuring out how to get the system into the desired overall state. You're doing more work in the short term, but it pays dividends in terms of maintainability.