OK, that's a valid point - however, copying and pasting from the Library/Application Support folder is just as easy (except maybe finding it).
Where I have a problem is that it violates the expectations of the platform. It's a Mac application - it has a Preferences GUI. This is not a problem with things like Apache, which, as a service, doesn't even have a front-end; I don't expect it there.
I suspect laziness on the part of the developer in regards to a Preferences GUI, rather than any attempt at a new paradigm.