Thanks. However, it looks like Vellum's store links feature works with only three stores: Amazon, Apple and Barnes & Noble.
I get that for direct uploads to all other stores, Vellum's Nook-Epub2 compile would work best. But I don't see "web links" written anywhere in the page you referenced with that Aggregators link. The advice just says if you're uploading to an aggregator, "your book should not contain any Store Links." I guess you can override the store link with some other kind of web link?
(Just so no one's confused, there are two Brads at 180g. We save money on card keys that way.)
You're right. Authors who are selling at Amazon, Apple, and Barnes & Noble can create a specialized ebook for each using just one Vellum file, but our Store Link functionality is currently limited to those stores. However, we have been hearing from authors who are finding success in additional stores (more than they were just a few months ago), so we are investigating expanding that list.
In the meantime, you can replace the store link with just a straight up web link, either using a separate file or changing the links before ebook generation. You can drag and drop an element of your book (e.g. your "Also by" page) from one Vellum file to another, so some authors just keep a master file with their back matter, similar to what you originally described.
What about print versions? Any plans to add the ability to export something that can be uploaded to Createspace?
(I'm sure you get asked this all the time, but vague hints at a future feature like that would really help me decide how many books to buy. Hint hint.)
As you've probably experienced, preparing a book for print is a very different process than creating an eBook, so it'd be a major endeavor. We don't have any plans to announce, but we're very much encouraged by the interest, and will keep it in mind for the future. Thanks for asking (and to others for seconding and thirding

).