Yeah, the threshold idea is better so I'm going to go with it. Even if I added more individual options, people only have to configure it one time, and then they're done until a new encounter is added. I don't consider it that bad.
After configuring all the Colliseum options to disable sounds from all abilities, only to have to go through them for Ulduar as well, I can only second the need for a 'global' config for alerts. Or at least a way less loud default. :-)