I know I’ve asked for this before, but it would be REALLY nice to have “back matter” moved to a first-class citizen on the level of front matter. These days, because of sample sizes and just general, modern conventions, most stuff is being moved to the back matter.
Scrivener supports a checkbox and allows you to select your front matter in the compile. Why not also support back matter? I mean, other than the fact that you guys have a list of a mile long of stuff to do. 
The main reason I didn’t add back matter to begin with was that front matter is more often different among formats (with different title pages and contents pages for printed material versions e-book material, for instance). But back matter does need to be different sometimes, and with more and more people publishing to iBooks and Amazon e-books, I think it’s even more the case now, with different links being added to back matter.
So, yes, this is on my list. I’m currently undergoing a complete rewrite of Compile (well, not a complete rewrite, but the entire UI is changing) and back matter is one of the things that is getting added. This is one big job that is part of an even larger overhaul, though, so it will be a little while before these changes see the light of day - possibly even next year. But it is coming eventually.
Back matter is definitely different per-compile, but I think most people are just doing what you pointed out: changing a link to a different store. I know this is what I do. Way back when, I was the one who requested that Replacements work on links as well so that I could do just this thing.
Of course, I only have a few books, so it’s pretty painless for me to generate a different .epub for each store with different links. For people with more books, this is much more difficult. I ended up writing my own piece of software to take a single .epub file and grind out a different one for each store after doing substitutions. Someone told me Vellum can already do this, but I love Scrivener too much to give it up.
I look forward to the new changes. I know how much work a big rewrite can be, so I won’t expect it anytime soon.