Use Accurate Spatial Extents
The more accurate the spatial extents you define when Opening and Selecting Data, the better the performance of spatial searches.
It will still find and process data regardless of these extents (although if they are orders of magnitude wrong the Build Topology task may encounter issues) but it will improve performance if they are approximately accurate to the data being tested against.
This will improve all Predicates or Operations which use the geometry as the first comparison, as well as the Build Topology task.
To see the current setting for the spatial extents, you can view the geometry attributes.