Why? It seems to me like it should be really simple: I prove I control domain X, they issue me a certificate for domain X. End of story. Does there need to be more?
I'll say this, I don't want to see "Let's Encrypt" go on some moral crusade deciding not to grant a certificate to a website because that website contains offensive content, but their job is to verify at least somewhat the identity of the requester to try and stem impersonation.
But that's a registrar problem, not a "proof that this connection comes from someone who controls that domain" problem. These aren't EV certificates.
Otherwise https only gurantees that you're actually talking to the domain you see in the URL, not who that domain belongs to.
Also, seizure and hijacking aren't equivalent.
Anyway, it's trivial to find out whether a domain was expired and re-registered. The date of initial registration in the whois will change, so you can just compare it with the value you saw when you first issued a certificate for that domain.