With the Supplementary Files intended, as stated, for data sets, research instruments, etc., the thought was that authors would only include them with the idea of publishing them. We had not forseen their use for referee's reports for an earlier submission at another journal, which was short-sighted of us. There is no way to suppress their inclusion, unless you suppress them all by not including the Supp File in the Reading Tools.
More importantly, perhaps, it should always be an editor's call, and not the system's, on what is suitable to be publish, so I will recommend that this option be included, at the Layout stage, in case, for example, the Layout Editor ends up including some part of the Supp File directly into the text.
Public Knowledge Project
University of British Columbia