Gary,
I have seen a few things fail after welding on it...whether or not it was directly related, I don't know. But I do know that some circuits that provide a ground for transmission control and other things can be affected. Another reason I have heard is that the arc can jump between the engine bearings, which is a possibility if the work clamp connection is made directly to the engine.
Given the radomness of electicity flow, seeking the shortest path to ground, the best solution seems to be keep the connections close, and follow every safety that you can.