Thanks for the clarification and highlighting my point with the comment about rbenv. I think I found the source of my confusion which is (http://www.joshstaiger.org/archives/2005/07/bash_profile_vs....) "An exception to the terminal window guidelines is Mac OS X’s Terminal.app, which runs a login shell by default for each new terminal window, calling .bash_profile instead of .bashrc. Other GUI terminal emulators may do the same, but most tend not to.".
That may explain why so many github projects recommend adding PATH and other env variables to .bash_profile.