Dot file and an adjacent identically named file without dot?

Is it bad practice to have a dot file and an adjacent identically named file without dot? --- Background: We already create a $HOME/.ourapp directory where we store various configuration files, log files, etc. but we are debating where to put files that the user would add, create, and modify, either from outside the app or from within it, using various tools. It would seem most natural have these in $HOME/ourapp but that might be bad practice or confusing.