Yes, I’m mostly speaking of packages here. Sorry if that was not clear.
Even in the case of a simple non-package project, the same problem could happen. Think for example of a research paper (like in this thread), where you might have a program to reproduce the results themselves and store them in data files, and another program to produce the plots shown in the paper.
Depending on the system where you want your program to run (for example on a supercomputer), it might not be convenient to install plotting packages there. The post-processing and plotting stage can then be run on an other system, where graphics dependencies are easier to install.