Hi there,
The set of roots that a Log accepts is entirely up to the operators of that Log. I can therefore only answer based on what we (the operators of the Google CT Logs) choose to do.
From our perspective, we regularly add roots to the set of accepted roots for our Logs to include all of the union of the Apple, Microsoft, and Mozilla trusted roots programs. However, we rarely remove roots from their set of accepted roots, so the presence of expired CA root certs is likely because they were once in the union of the Apple, Microsoft, and Mozilla trusted roots programs, but no longer are. We currently use the same set of roots for (almost) all of our production Logs, as it simplifies deployment, which is why the newer Logs still include these expired certificates. However, this point has recently been raised in our team internally, and we are considering changing this for new Logs. Of course, making this change requires work, and there is a question of prioritization of the work we currently have on, so we can't guarantee this will happen any time soon.
Hopefully that answers your question!
Kat & the CT team at Google