Panels Skin Specfic?
Using Jamroom
My thinking was this.
I have a short attention span and like to switch between multiple skins I am tinkering with and if using site builder you really need a separate install of jamroom and the associated modules if you want to design multiple skins at the same time.
With panels being site specific you would have to export, import another set when you switch skins and then again and again. If they were skin specific this wouldn't matter as each skin would have a unique set of panels attached and switching between them would auto load the appropriate panels.
Now I realise I might be only one of a very few people that work like this, so hope you can grasp what I am saying here.