I think dot files in home directory for configuration files are fine, especially if the user creates the files themself rather than the program created them (although sometimes a program may wish to create a user cache file, for example Free Hero Mesh creates a file ~/.heromeshsession by default but you can configure a different name if you wish; also some programs such as web browsers may store cookies and so on, although you should be allowed to reconfigure that, too). A program might also support a command-line switch and/or environment variable to override what file (in what directory) to use.

Requiring files in your home directory that do not have a dot at first (with a fixed name) is no good, though.