If you trust VLC and you trust the video file you're watching, then turn the master audio back up during the loud "Universal Pictures" intro or whatever is an equivalent introductory sound at the beginning of the movie you're about to watch.
On my chromebook, there are two volume buttons and one mute button that are by far the most convenient way to adjust (master) audio for such a situation. So you turn down for random browsing and turn up for watching movies or whatever.
Btw-- those are almost certainly the controls someone would use to turn down or mute the sound of that horrible website audio listed above. In such a case the fact that pulse can give you an app volume for Chrome doesn't help anything-- for example, the user who adjusted Pulse app volume down to avoid pain will need to adjust it back up when watching a movie on Youtube for the same reason you mentioned. But they can't adjust the app volume with the keyboard controls. So to make use of that feature forces a more complicated UI that takes longer to use.
* default Alsa setup: set master to level that seems comfortable-- i.e., "to taste"
vs.
* default Pulse setup: set Chrome's app level to taste
Bug: packet.city plays an annoying sound with a perceived loudness that the user did not predict.
* Alsa solution: lower the master volume to a level that doesn't result in painful output from packet.city, and adjust all other apps accordingly
vs.
* Pulse: lower Chrome app audio, but leave yourself open to similarly unpredictable painful events from other apps
It seems in this case that the limitations of Alsa actually force the user to do the safe thing wrt perceived loudness.