You're probably right, actually, but I also need some space for XP/Rep bar, stance buttons and a pet bar, even if the idea is that the pet will be controlled using the action bar anyway. I'd also like it to somehow feel like one big bar, instead of free floating clusters spread all around.
One of the issues I think new players have with controller gameplay is the bucket load of bindings that are just handed to you (although you're of course free to configure your setup however you want) and it might be cumbersome to keep track of it all for a beginner. Having played with this setup for quite some time, I still look at my bars occasionally since I don't always remember all my spell bindings. I'm aiming at providing a little bit of both worlds; all your controller bindings are always visible, but in a way that's not taking up the entire screen and (ideally) only uses icons and short text strings.
Placing the modified buttons under the main button and moving the hotkey indicator actually looks alright though:
Btw, this is what the bindings look like without the extension enabled:
Weirdly enough, the extension shows 4 more bindings, but it looks like a lot less. Might be because of the menu bar, pet bar and bags though.