My current threejs version is “103dev” (as defined in three.js file) I use Physijs in my game extensively without any issues. It is no longer under active development so that’s what you get.
For me the biggest advantage is the syntax below, where both the primitive physics and threejs shapes are created. Just simplifies my dev.
var box = new Physijs.BoxMesh( new THREE.BoxGeometry( 4, 4, 4 ), box_material );
While navmesh is intriguing, the only way I have to generate one is with a back level blender. The newest release does not (or didnt when I checked) support the generate navmesh capability.
If you are running around, collision support simplifies triggering particles, sound effect, etc.