Why might one add ~/.profile to ~/.bash_profile?

.profile and .bash_profile are identical in terms of when they're meant to be executed: they're executed when you log in. The difference is that only bash runs .bash_profile; Bourne-style shells (dash, ksh, etc.) runs .profile. Bash itself runs .profile if .bash_profile doesn't exist.

Even if you have bash as your login shell, .profile is often the one that's executed when you log in in graphical mode — many distributions set up the X session startup script to run under sh and load .profile.

Hence the advice to use .profile instead of .bash_profile to do things like defining environment variables. Unless you absolutely need bash-specific features, just put everything in .profile. But even if you do, there's a reason to keep a .bash_profile, which is that when bash loads it, it doesn't load .bashrc, even if it's interactive. Hence, for most people, ~/.bash_profile should consist of these two lines:

. ~/.profile
case  $- in *i*) . ~/.bashrc;; esac

You should not run xmodmap from .profile. This isn't executed when you open a new shell, but it is executed, for example, when you log in remotely with SSH with X11 forwarding. Unfortunately, there's no standard file that's loaded when you log in in graphical mode. Debian loads ~/.xsessionrc (I think this applies to all display managers, except Gdm which loads ~/.xprofile instead); other distributions have different setups. If you need cross-distribution portability, it may be easier to configure your desktop environment to execute xmodmap when it starts. If all you're doing is swapping CapsLock and Ctrl, this can be done with XKB settings that most modern desktop environments provide an interface to.

Remember that bash(1) is the only shell that reads .bash_profile, other Bourne shell derivatives just read .profile. If you sometimes use another shell, you'd want to keep .profile.