The configuration files are handled differently: updmap e.g. has an additive concept: it will use all updmap.cfg it finds. On the other side dvipdfmx will use only the first dvipdfmx.cfg it finds.
In the second case it is problematic when the template for the cfg (e.g. dvipdfmx.cfg.template) is empty. If a user opens with
"initexmf --edit-config-file dvipdfmx"
the local cfg and adds e.g. "p letter" to change the paper size he will loose all other settings from the global cfg like the name of the fontmap and the settings for ghostscript.
I think it would be better if in such cases the template were a copy of the global cfg -- and if starts with a large warning that if this cfg exists the global one is ignored.