Short answer: Yes, you can rotate it.
Long answer: If you want to do isometric stuff, the 3D Box isn't going to help you. The 3D Box will always be in perspective relative to the viewport regardless of it's rotation. This means that you can change the yaw of the box to 45 degrees, but you will still be able to see under it if it scrolls towards the top of the screen, or the left side of it if it scrolls to the right side of the screen. Also, the box itself doesn't collide with the faces of the render, but rather a 2D mask created by the back face texture that is always oriented toward the viewport.
Still, you can rotate the box however you like. In the Event Sheet editor, select one of the following actions:
New Action -> 3DBox -> Set yaw
New Action -> 3DBox -> Set pitch
New Action -> 3DBox -> Set roll
Each of the settings takes a positive or negative floating-point value in degrees.
The 3D Box object isn't so much a feature as it is a proof-of-concept. It does have it's uses, but they are rather limited. Mainly it's there just to show that it is possible to integrate 3D into Construct. If I remember correctly, there are plans to eventually add more 3D support for Construct, but not until after v1.0.