PS yahoo is the worst for assuming poor reputation from a sender. In my experience they just introduce massive delivery delays at the drop of a hat even when the sender has a stellar reputation.
You're right in one more way: both Google and Microsoft offer email hosting solutions for small businesses. Their main (and, if you've got more than 8-10 accounts or so, the only) selling point is that it makes managing email hassle-free. Making it as painful as possible for small businesses to host their email server helps these services tremendously. If they had real interoperability (either of their own accord or because it were forced upon them through regulatory measures), the biggest cash cows of these services -- companies that are well into "enough accounts that your own server would be much cheaper" territory but not large enough to afford or risk large infrastructure changes -- would evaporate pretty quickly.
But to reiterate my earlier point: Google and Microsoft have the computational and storage capacity to have a detailed history of all domains' authoritative mail servers behavior. They will know whether a domain has a history of patch negligence.
No, I think the far simpler explanation is that they just don't bother tracking reputation by domain. Or if they do, it's largely overshadowed by the weight given to IP-based reputation.