It's the same in that way, yes: both are federated protocols where you need to trust the owner of your server. But with Mastodon there are within-server interactions like the local timeline (https://cfenollosa.com/blog/you-may-be-using-mastodon-wrong....) that have no equivalent in email, so if you decide to try to avoid this risk by self-hosting you're giving up something that a lot of Mastodon users really enjoy.