Your sketch on the left is the proper way to do a tube joint, it provides the highest stiffness and strength. It also can be the most difficult to fabricate which is why you see many chassis with tube joints that look like your sketch on the right. A good example of proper tube joint design and fabrication are the present day off road race trucks, take a look at the effort they take to ensure the proper tube alignment for the fabrication of their chassis. These frames are probably the most sophisticated tube chassis used in racing today and a good example to follow.
If you want to do it right use the left sketch method.
Rex