Hi,
1. You can turn off the "force canonical URLs on listings" setting.
As long as the canonical URL is filled in, search engines won't flag your pages as duplicate. That option is only so that your customers always have the same URL on the product pages, which is not what you want in your case.
2. You mean based on the domain name where the purchase is made ?
You need to check the domain name of the URL in the code of the emails that you can edit via the menu System>Emails
For example:
<?php
if($_SERVER['HTTP_HOST'] == 'domainname.com'){
echo "something";
}else{
echo "something else";
}
?>