There's really nothing to be left to interpretation. They're saying that if your school has a pre-health committee service, you have to use it.
Your school's committee should have LOR requirements that are in line with med school requirements (i.e. they should require at least 2 science letters in order to cover the bases set by med schools). Mine required 3 science letters, one of which could be research, and 2 more letters that could be science, non-science, or character references.
If you're worried about them seeing the lack of 2nd science letter, give the school an anonymous call and just ask if the 2 letters are still required with the committee letter. Not sure why people are so afraid of doing that.