Will HFNetCheck still allow people to pick and choose MSBulletins and/or KBs? Also will Shavlik be working with BMC so their BladeLogic tool which, uses the HFNetCheck engine to patch, allow for their customers to patch using the features BladeLogic allows for; such as, some teams create smartgroups to patch just based off specific KB's as well as other customized patching.
You should contact BMC support for this. What I can tell you is our scan engines are at the mercy of how Microsoft releases patches we can't perform any magic to pick and choose updates included in roll-up patches. And yes, this will adversely affect using filters to ignore or specifically scan for individual patches.