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I actually think that building an independent system for binaries is a better plan, for various reasons.

One is that log bloat is indeed a problem, not so much for the logs, but for those that want to monitor them.

The other is CT has made some tradeoffs to allow cert issuance to be quick. I don't believe binaries need the same tradeoffs, and, for example, instead of an SCT, they should come with an inclusion proof (something I'd like to see for certs, too, in the long run).