I think this is really Amazon's fault but I'm filing a bug in case it's something that you're interested in working around. I am told that if you visit Amazon.com in the United Kingdom, Amazon.com displays a banner suggesting you visit Amazon.co.uk instead. (Many non-Amazon sites automatically redirect you to their country-specific site unless you explicitly opt out.) This is a bit of a problem if someone wanted to distribute a webapp, say using Epiphany's webapp mode, where it would be bad to routinely show the user the wrong page. And it's also bad for other reasons to have several different webapps for each supported country and let the user pick the "right" one. Ubuntu worked around this with their Unity implementation (which did not use webkitgtk at all) with a bit of JavaScript in front of their browser that would attempt to load the correct country web page. You can get a list of the country versions by visiting an Amazon webpage and clicking the country link(s) at the bottom.
Yeah, I don't think this really has anything to do with WebKit.... It's not an issue for Epiphany either, because web apps by design rely on you knowing the right domain at the time the web app is created. amazon.co.uk and amazon.com are just completely unrelated domains. You're going to need a custom desktop file that launches a wrapper script that picks the right URI to use when launching Epiphany in web app mode.