It's a problem, but for all the problems with Mastodon I try to think of the equivalent problems with email (since I think it's the analogous for federation). What keeps you from having github@example.com for your own domains?
It's just a matter of expectations and messaging to all the users they're onboarding all of a sudden, but email is a good analogy, in fact if you control your email domain and your own mastodon instance, they could be one in the same address!