Currently, CT logs have a list of roots that may submit to their log. If you run your own self-signed CA, you cannot (usually) use these logs, and there is a lot of effort and little benefit to running your own log setup.
CT tries to protect relying parties from bad issuers, but when the relying party is the same person as the issuer, it is not as beneficial.
Requiring CT universally, even for "private" CAs, provides detailed evidence for several kinds of problems, such as various laptop vendors who have pre-installed MITMing proxies. It doesn't prevent those kinds of behaviors, but it makes denials less credible.
When a laptop vendor is building the device that's being shipped, I don't think it's practical for a browser vendor to be able to expect to win that arms race.
> It doesn't prevent those kinds of behaviors, but it makes denials less credible.
Once you start doing more malicious modifications of the browser, it should be more obvious (to both you and anyone observing or doing forensics on your behavior) that you're doing something malicious.