I'm currently writing some documentation for Kaiser and while digging into the tool's internals I missed the ~/.kaiser/.config.yml for quite a while.
Since ~/.kaiser is already a hidden directory, I think the files in there shouldn't be hidden. I suggest changing it to ~/.kaiser/config.yml and building in a little backwards compatibility layer for people that still have the old .config.yml I'd suggest a function that looks for the dotted file and undots if it exists. If an undotted config file exists already, it should take priority over the dotted one.