No, nobody is shutting down WoW to load another Character Set, unless they don't know the following: All you need to do is log out to Character Select, select the new team from the launch menu, then log into the new (matching) characters in the game from there.

As far as the issue with your Window Layout, it sounds like you may not have done an Export since upgrading? The behavior you're describing is expected until you do. At worst, you can run the Window Layout Wizard (right click on Window Layouts) and replace your current Window Layout with a newly-generated one.

And as far as the ISBoxer Addon giving that warning box... because of the way you are designing your configuration (to not rely on the Character names), you can safely ignore it and click it off. In build 38.2.312.1 or later (not out yet as of this post) you can put in a * for the "Actual name" field per Character to make it ignore.