As imperfect as PatchFinder may be, I think it's batting average is higher than relying on Build Numbers, especially from applications other than ArcGIS Administrator. Looking at FAQ: What are the build numbers for releases of ArcGIS Desktop?, one can see that build numbers for ArcGIS 10.1 SP1 QIP are incorrect in ArcMap and ArcCatalog. The ArcGIS 9.3.1 SP2 QIP had a similar issue.
Taking the above information together with the fact that most patches don't update build numbers, our organization has moved away from using build numbers for identifying anything beyond major/full releases. In fact, we have an Esri Support Case open right now over how to definitively show the OpenSSL patch has been applied because PatchFinder isn't showing the patch on some machines that it has been applied on.
Of course, the issue only gets muddier when dealing with patching Background Geoprocessing as well as Desktop. Just be aware that identifying installed patches has historically been as much an art as a science.