Can you mention any single project which only does one thing?
Let me look at some examples:
Both an interactive user interface, and a scripting environment. And while the different programs running in bash often do communicate together, they do this using undocumented apis in the form of text output which is the worst way of module communication.
It also confuses matters because the user-readable output from running a command in an interactive bash shell is part of that apps api. Just think about all the problems this causes for api updates, and translation of output to other languages.
Is composed of a server, and lot's of modules, but none of the modules can be used outside of Apache. This looks to me like what systemd does, but nobody ever complained about this.
Don't even get me started. Its a compiler collection of parts which depend on each other.
The linux kernel:
Refuses to maintain a stable api, so unless your module is part of the kernel itself, it will break at every linux release. Not modular at all.
None of the tools/effects which gimp uses are independent modules.
There were never a modern desktop/server linux distribution using what is refered as the "unix way"