I'm sorry, but this is not a flaw in the interface, A:M is designed to open only the toolbars that are needed for the current window open.
Here's an example, if you hide the modeling toolbar in the modeling window, it will disappear. If you close the modeling window, open a chor window and select the modeling toolbar, when you press OK it will disappear, BUT if you reopen the modeling window, the toolbar is now there.
The A:M programmer is not likely to change this. Having all toolbars open in any window is not user friendly IMO and probably to most other users as well. It will just clutter up the interface and confuse the user as to what tools they need in the window they are using at the time.
As you mentioned before, you can create your own toolbar, with any tools you wish, customized to your liking.