That's correct: the Galley version(s) is what finally appears in the Table of Contents. You can upload multiple Galley files, for example an HTML and a PDF file, and they will appear as links in the ToC.
At the moment it's not possible to customize galley file names, but this has been marked as a feature request: http://pkp.sfu.ca/bugzilla/show_bug.cgi?id=3231
I'd suggest keeping track of that, and also adding further comments if you have implementation ideas.
You may want to search the forums for other discussions on using OJS' public id system for some general background as well -- it won't solve your problem, but it'll give you an idea on what other steps can be taken.