Here's where it gets a little more odd. I rebooted my Mac and the problem is gone. It's now working the way I would expect it to. Weird that if something was quirked in the OS only Blender was affected by it rather than other apps as well. Sorry for taking up so much of your time. Now I get to watch some tutorials and try figuring out this beast.

Guess I'm just special? :)

I have no idea what "separate spaces" is. Simply downloaded the latest release of Blender (first-time download), moved the folder to Applications, launched the program, opened User Preferences, changed Input Select from "Right" to "Left", clicked "Save User Settings", then closed (or rather tried to close) the preferences window (doesn't matter how - all have the same effect: red close button, command-w, Windows->Close) and the application quits. If I thought Blender was bad then I wouldn't have downloaded it to try it out after hearing so many good things about it, but the user-interface is overwhelming compared to similar applications and having the application quit when closing preferences is pretty much a blocking issue.

I found the startup.blend file down in Application Support and deleted it, as well as userpref.blend but there is still a bug in the application. Upon launching Blender the preferences no longer auto-displays but then opening User Preferences, making changes, saving the settings, then closing the preferences still quits the application instead of just closing the preferences window. (Were preferences tested before releasing the program?)

Agreed, should not happen. Where would that startup.blend file be located at?

Btw, this is on a MacBook Pro Retina Late 2014, the newest model released.

Let's see if a screen capture will work...

Now also when restarting Blender (frequent when trying to close the preferences window and forgetting that it closes the application) the preferences window is always open by default and is titled "Blender" instead of "User Preferences". My first day using this application and already thinking of dubbing it "Blunder" based on its user-interface and poor (low-contrast) default color theme.