If they assume that most users apply all "critical" Windows updates in the order that they're pushed, the anti-virus vendor could snapshot their reference PCs before each update and record the hashes of all Windows files. It's possible to determine which updates have already been installed on a machine (there's an option for this in the control panel, and the information is probably stored in the registry).
As for different versions, it doesn't seem like this should be a significant challenge to an organization which already has to maintain a test OS farm. The process of updating after a release is mostly automatic and if this acted solely as a guard against false positives, the consequences of missing a patch permutation are the current status quo.