There are at least two (and probably many more) answers to this question, one from the viewpoint of the creators of the film and one from the viewpoint of the characters.
The following explanation can be found in the official Buckaroo Banzai Fan Club World Watch 1 Newsletter from the April 1986 edition. This was written by Director W.D. Richter :
"I can only imagine Buckaroo trying to grapple with this question. When cornered (as I feel now), he often quotes H.L. Mencken's nasty remark about how every complex question always has a simple answer...that is usually wrong. But it is high time poor New Jersey's honest inquiry be answered. Let me rephrase the question first one way, then another. "Why is a watermelon trapped between those monstrous pressure plates deep within the Institute's Critical Stress Laboratory?"
Team Banzai botanical agronomists have been for years hard at work on the problem of hunger in Third World countries under constant revolutionary turmoil. A non-political, humanitarian effort, their goal has been to find ways to feed starving peoples in remote areas where traditional food delivery systems prove woefully inadequate. Often the only way to get the nourishment into the bellies of the needy is to hit and run, avoiding all petty ideological side-taking.
What you see in the Critical Stress Lab is a revolutionary watermelon capable of withstanding impact pressures of 300,000 pounds per square inch! Sweet, juicy and vitamin-packed, this remarkable fruit can be dropped from the bomb bays of low-flying aircraft into the backyards of disenfranchised villagers in the remotest backwaters of this angry planet. Just another Team Banzai effort to cut through all the unnecessary crap around us and help people help themselves. Look for high-impact, low cholesterol eggs next... and sooner than you think, shatter-proof whole-wheat taco shells.
[The question that this all brings up is, of course, if you create a watermelon that can withstand the impact from being dropped from an airplane, how do the people that find it open it up? - Sean]
Rephrasing Number Two: "Why is there a watermelon in the movie at that particularly tense moment? Doesn't it clutter the narrative flow?" Absolutely, it does, in answer to part two of your question. But isn't life full of things that get in the way?
Those of us making the movie that day felt under particularly severe pressure from forces who would rather we'd all just stayed in bed. Not much of what we were doing didn't clutter the movie. With a mountain rushing up in our faces, was there any point in putting on the brakes? Would Buckaroo put on the brakes?? Would a watermelon in the midst of a chase sequence not be, in its own organic way, emblematic of our entire misunderstood enterprise? At once totally logical and perfectly irrational?
Exactly. We knew it would confound and upset certain authoritarian types. So we did it. And it worked."
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