I can think of a few reasons I like the auto-destruct...First, it can prevent people from deliberately blocking new vehicles. Driving a Mammoth Tank into the War Factory, thereby making it hard for new vehicles to come out; Parking a Stealth Tank right on the Airstrip circle so that any new units land on you (when they're dropped from the cargo plane) and then either take forever to touch the ground, or tip over and explode. Things like that.
In some games, I've seen my own teammates drive a vehicle into the gate area of the Tiberium Refinery and just leave it there. Then, when the Harvester returns, it just keeps on bumping into the vehicle, unable to unload any resources or go out to collect more. Those are the same people that might try to jam the vehicle factories if they were able to. Of course, it wouldn't matter if you were in a good team, but that's not always the case...
And also, it's a great way to trash unwanted vehicles. If, for example, you find a unused MRLS lying around that nobody wants, you can drive it back into the War Factory to prevent the enemy from stealing it. Once another vehicle is purchased, the MRLS will just go boom.