I opened the ticket because this looks/looked like it may be a regression. It may yet be, but the removal of over-nesting is always a "Good Thing" so I would highly recommend you proceed
As you see, the "over" part can be a question at times. There are cases where nesting is necessary. In those cases, you may just need to specify the layout (typically "fit" if you have a single child item). If you don't specify a layout config, you get the "auto" layout which does not manage the size of the child items in any way. It does react to their "auto size" but that can be confusing to understand the "auto size" of a bunch of child components. Often this is not what you want, but could be.
If the nesting is intentional, I would also highly recommend a comment stating the reasons (such as "need panel header/tools inside the tab") or something so the next person to maintain the code does not "fix" the problem by removing the nesting.
I would also suggestion adding "layout: 'auto'" to any place where that is specifically what you want, again because it often looks like a mistake when you don't specify the layout.
While one could argue this more broadly (I mean, there are other config properties that have default values), over-nesting and unintentional use of "auto" layout are very common mistakes.
I would stop on that error in the debugger (Chrome or Firefox/Firebug make this easy) and see if you can tell from the callstack what is attempting to happen. If you cannot figure it out, posting the callstack here may help others understand the situation.