no there is no real reason why routing in Pastry is that slow. The KBR interface only defines the method signature (for example the route method). The implementation is the responsibility of the overlay. Due to the fact, that the development of PeerfactSim.KOM is going on for years and many different developers have added different overlays, there exist some very large differences in the internal implementation and also in the use of messages.
If you need the same internal handling for comparison purposes, there’s no way around the revision of the overlay.