Speculating a bit out of my depth here, but I'm under the impression that most of those sometimes-configurable OS-level CA lists are treated as "trust anything consistent with this data", as opposed to "only trust this CA record for these specific domain-patterns because that's the narrow purpose I chose to install it for."

So there are a bunch of cases where we only want the second (simpler, lower-risk) case, but we have to incur all the annoyance and risk and locked-down-ness of the first use-case.