Short answer-Yes.
There is a lot of inefficiency in engines, but none of it comes from fuel molecules being "misaligned." Assuming the magnet somehow actually affects the fuel in the first place. But, if you're really getting it for free you can do a good A-B-A test on it to prove what the engineering already says-that it will have no effect. But most of the people on this website probably already think its BS and the true believers may still hold out based on their buddy's completely unscientific test with 1988 Toyota Corolla