These are commonly called "cluster joints". As you have seen, they can require some thought before any tubes are even cut. In a perfect world every joint would be 100% welded (if desired) but this is difficult and often impossible to do. A properly designed chassis will have the joints under compression as much as possible. This reduces the liability of incomplete welds and reduces stress on the welds that are in place. While it may seem as though leaving as much as 1/2 of a joint unwelded would result in catastrophic failure, in a properly designed cluster joint this missing weld area has virtually no effect on the overall joint strength and, in some cases, could lead to excess distortion and residual stress if fully welded.
An excellent book on steel tube structures is published by the Experimental Aircraft Association and is titled "EAA Aircraft Building Techniques: Aircraft Welding". It mostly covers gas welding and thin wall 4130 steel, but the general ideas of tubular structure layout, joint design, and tube fitting are the same as when building a race car.