Sorry I removed old entry about this thing by mistake. This entry is updated version of it.
Add following configuration in your init.el. Then exec-path-from-shell does not warn about environment variables.
(custom-set-variables '(exec-path-from-shell-check-startup-files nil))
Recently exec-path-from-shell warn if environment variable in interactive mode is different from them in non-interactive mode. I suppose this is right. We should set environment variables in .bash_profile or .zshenv, not .bashrc, .zshrc. However this is not easy for some configurations such as rbenv. rbenv initialization eval 'rbenv init -' generates some environment variables setting and function definitions. We should not define functions in .bash_profile, .zsh_profile so I think such setting should not be moved. And I want to keep shell configuration in only one file :-)