Please take a look at line 1936 in main() function in sshd.c. 

/* Find matching private key */
	for (j = 0; j < options.num_host_key_files; j++) {
		if (sshkey_equal_public(key,
			sensitive_data.host_keys[j])) {
			sensitive_data.host_certificates[j] = key;
				break;
			}
	}

the sshkey_equal_public() is trying to compare a cert's pub with a private key, and it never find a match which makes sshd cannot use this certificate even though its private key is in ssh-agent.
I believe it should be comparing a cert's public key with a public key in sensitive_data as follow.

/* Find matching private key */
	for (j = 0; j < options.num_host_key_files; j++) {
		if (sshkey_equal_public(key,
			sensitive_data.host_pubkeys[j])) {
			sensitive_data.host_certificates[j] = key;
				break;
			}
	}

https://github.com/openssh/openssh-portable/blob/V_8_4/sshd.c#L1936