Not a CouchDB dev, but I figured I'd throw something into this discussion. I encountered this behavior some time ago too, but I don't think that there is a problem in _read_ order. In fact, the current one is in line with what I and hopefully others would expect (*.d directories usually overrides the stuff above them).
What is wrong is the place where (some) _writes_ go. Don't know if possible, but, continuing in your example, changes in geocouch config should go to geocouch.ini, other changes to local.ini. Or maybe changes to existing key should go to the file from where it was effectively read, new keys to local.ini. Or maybe this is way too complicated :-) Just my 0.017 cents. LT
