I should also emphasize that I'm not proposing this for technical reasons. The sentence where I clarify this is now bold in the post.
Doing what you propose would only bring extra clutter to those who do not have the social problem that you propose to solve with the technology.
Explain the hypothetical boss it is a bit like an ELF format, but for configuration. He does not recompile every executable every time before running it, does he ?
Also, this is not the first time this design decision has been made - as a well-known example you can bring up Chrome and Firefox.
One thing where your suggestion does make sense is where one has to frequently re-edit the config file and restart the server. But that is solved by writing the shell scripts, not by cluttering the core code base, IMHO.
That's a good point. Mongrel2 config files == .c files, m2sh == make, config.sqlite == libmycodez.so