Currently there is not a user-facing way to modify the fixed tranform on the robot base - it's always assumed to be at the origin. This could be a future enhancement.
For now, to work around this, you can use addSubtree function to get around this limitation.
lbr = loadrobot('kukaIiwa7');
kinova = loadrobot('kinovaGen3');
kinovaMoved = rigidBodyTree;
rb = rigidBody('newBaseForKinova');
The result can be seen in the image below. Note that addSubtree does not preserve the Base of the rigidBodyTree object to be added - as a result, you can see that the Kinova arm's base mesh is missing, but everything else should not be affected.
To fix the visualization, you can call kinovaMoved.Base.addVisual(...) , if you have access to the mesh STL file.