There is no need to use the 3-d panel if you only want 3-d cockpit.
That might be the most counter-intuitive statement in the entire universe. Let's break it down and see what's going on. Originally we had the 2-D panel. The 2-D panel was where you put your instruments for interior views. When 3-d cockpit support was added, the 2-D panel was used to create the panel texture - that is, the instruments texture for the 3-D cockpit.
Thiat worked for a while, but as handles became more complex, screens became larger, and as 3-D cockpits became a more complex, authors started to run into the system's limitations. If the author wanted to create a huge panel, then the panel texture for the 3-D cockpit was huge. Furthermore, texture space for the instruments in the 3-D cockpit was wasted because the 2-D panel had to have windows on it.
With X-Plane and 9 we added the 3-D panel to fix these problems. The 3-D panel is a second panel whose sole purpose is to provide instruments as a texture for the 3-D cockpit. When you have a 2-D panel and a 3-D panel, the 2-D panel is used to draw the panel in 2-D viewing modes and 3-D panel is used only to create the panel texture for the 3-D cockpit. With this setup the 2-D panel can be huge, and the 3-D panel can be small and compact with no windows.
The 3-D panel solves a second problem as well. Often the overhead panel is drawn in perspective on the 2-D panel this perspective view is useless for texturing a true 3-D cockpit. With a 2-D panel and a 3-D panel, the author can draw the overhead in perspective for the 2-D panel, and orthographically for the 3-D panel.
Now here's where things get complicated: if an airplane has no 3-D panel the 2-D panel is used for both the 2-D view and the 3-D cockpit. But some airplanes have only a 3-D cockpit. In this case, there is no reason to use the 3-D panel at all. You can simply use the 2-D panel for texturing the 3-D cockpit and not worry about the user seeing it; in a 3-D only plane the user will only see the panel as a texture for the 3-D cockpit.
This setup is confusing in name: how can you have a 2-D panel used for a 3-D cockpits? But it is an allowed configuration. In fact, it was the only configuration allowed in X-Plane 8.
In summary: a 3-D cockpit can use the 2-D panel or 3-D panel as its panel texture. If an airplane has no 2-D panel, then the 2-D panel can be used for the 3-D cockpits without problems. In this situation and there is no need for a 3-D panel.
(It might be better to think of the 2-D panel and three panels simply add his two panels so that you can have two different versions of the panel. The names to the panel and 3-D panel are really just labels.)