All a custom domain changes is your domain; you are still bound by the code and conduct restrictions of WordPress.com. Essentially, if you have a custom domain you have two URLs: whatever.wordpress.com and whatever.com. They both work, so there’s no effect on the old incoming links. The only problem is that they give their googlejuice to the old URL and the new one starts again from zero, so many people contact the people who’ve linked to them or blogrolled them and ask them to please change the link to the one reflecting the custom domain. But most people won’t change it.
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