Great that lets encrypt gets funding, long may it continue!
But this might be the first time that a company has sponsored a CT log without operating that log itself.
>> CT logs are already chained
Trillian is a centralized Merkle tree: it doesn't support native replication (AFAIU?) and there is a still a password that can delete or recreate the chain (though we can track for any such inappropriate or errant modifications (due to e.g. solar flares) by manually replicating and verifying every entry in the chain, or trusting that everything before whatever we consider to be a known hash (that could be colliding) is unmodified (since the last time we never verified those entries)).
According to the trillian README, trillian depends upon MySQL/MariaDB and thus internal/private replication is as good as the SQL replication model (which doesn't have a distributed consensus algorithm like e.g. paxos).
A Merkle tree alone is not a blockchain; though it provides more assurance of data integrity than a regular tree, verifying that the whole chain of hashes actually is good and distributed replication without configuring e.g. SSL certs are primary features of blockchains.
PKI is necessarily centralized: certs depend upon CA certs which can depend upon CA certs. If any CA is compromised (e.g. by theft or brute force (which is inestimably infeasible given current ASIC resources' preference for legit income)) that CA can sign any CRL. A CT log and a CT log verifier can help us discover that a redundant and so possibly unauthorized cert has been issued for a given domain listed in an x.509 cert CN/SAN.
The CT log itself - trillian, for Google and now LetsEncrypt, too - though, runs on MySQL; which has one root password.
The system of multiple independent, redundant CT logs is built upon databases that depend upon presumably manually configured replication keys.
Does my browser call a remote log verifier API over (hopefully pinned with a better fingerprint than MD5) HTTPS?
Now, from a security point of view, it only takes breaking into one issuer to issue bad certificates. But maybe classifying everything as either centralized or decentralized is too simple?
That said, that's just because both use Merkle trees. CT isn't a blockchain.