From the Mode Panel, you are able to drag into the level a special actor called Nav System Config Override.
This actor allows you to override the built-in Navigation System by using another one. Of course, you will have to develop it first, and this would need a lot of effort.
Reasons why you should substitute the default Navigation System (or maybe used along with another one) is mainly due to overcome limitations. What about air-units; how can they do a 3D Pathfinding? How about spiders who have a surface pathfinding?