They know you've taken the COMLEX. Even if they don't put much stock in it, I'm guessing programs would view withholding the score as a sketchy move and assume you're hiding something (which, well, you are).
My guess is that for most ACGME programs, as long as you've passed COMLEX (ie they don't have to worry about you getting a license), they'll be happy to look past it at a great USMLE. But I'm just a fellow fourth year so my speculation is truly just that.