If you enable the Research Support Tool, supplementary files will also be publicly downloadable from that -- so perhaps not the best use for review material (although as a Director you can remove or replace a supplementary file).
I haven't been able to replicate your specific problem: if I allow for supplementary files to be seen by a review at time of submission, there's a link to the file under the article file as well when a reviewer logs in and checks the submission file out.
I'm wondering if perhaps there's a better way for you to use the submission process, mainly to keep all review material in their proper place. Would you be able to require an "abstract and proposal together" (under Conference Setup Step 2), where you define the proposal as your two-page PDF; and then down the road if you want a longer paper, mark the submission as revisions requested, whereby the author would have to upload a longer author's copy.
If I'm missing something, please let me know -- and if you absolutely need to use the supplementary files route, we can debug further.