It says on the bottom of the page that prepack optimizes for performance/less computation while closure optimizes for file size.

Closure Compiler does much of the same things; but I think prepack is looking to do considerably more compile-time evaluation; closure compiler only does some of this.

I think prepack will also generally generate larger, bulkier code than you might get out of closure compiler. When I give prepack code from closure compiler, it seems to make the code much larger but change nothing. Your mileage may vary.