It won't help much in general, unless your recommender is reputable in the department you are applying to. That being said, it will be very hard for a professor with a narrow regional focus to be widely recognized.
Seriously? I think MIT's system is stupid. I couldn't help but laughed out when I saw the LOR system. Dude, it's 21st century, and we are still emailing links by hand? I just can't believe this is happening.