The problem is that you may not know exactly what the URL to a specific file will be before you publish it. One workaround is to use unique identifiers for all components under Journal Setup Step 4.3, and use an increment-able naming mechanism to name these components; then you can string the components together to form a URL. For example, if your journal is at http://example.com/index.php/journalName;
the public issue identifier (set under the Issue Data page for that issue) is set to "1v1"; the article public ID (set under the Table of Contents page for that issue) is set to "article1"; and the supplemental file public identifier (set by the Editor when adding/editing a supplementary file) is set to suppFile1, then you can add the bits together like so: http://example.com/index.php/journalName/
+ [article public ID] + /downloadSuppFile/ + [supplementary file public ID]
... which would look like: http://example.com/index.php/journalNam ... /suppFile1
So long as you name each article and supplementary file using some sort of understood mechanism, you should be able to build the links for inclusion before you publish them.