It's not an ideal solution to your problem since you asked for one that doesn't involve the use of an addon, but I found that if I use the default UI to set up my totem bars, bind their activation to a hotkey, and then use Bartender4 to arrange the bars the way I want it works quite well. As of yesterday (the last I checked) Bartender4 hasn't been updated since the patch so there isn't even an option to display the totem bars yet (if ever). They're basically perma-hidden because it appears to fall under the same classification for BT4 as a warriors Stance bar, and BT4 automatically disables the stance bar portion of the interface for shammies.
Either way, it allowed me to set up my totem bars without sacrificing my prefered layout. Bartender is pretty easy to use so even if you just used it to mimic the stock UI and set things up that way, it might be a solution.