Because they both work but kind of cumbersome to access and it seems that if the application stops playing audio the volume would reset itself. That's very annoying when you want to lower the volume when you want to listen to an album on SoundCloud (its web player doesn't have a volume control widget), and the next track is unbearably loud again.
When you are playing audio via different applications, go to Sound option from system settings and select tab Applications. Then you will be able to see volume settings for each applications that currently play sound. eg: vlc player, Alsa audio plugin etc. You can then set volume for each applications.
Hope this might help you.