My understanding is no. In order to run with the back end being either OpenGL, Vulcan, or Metal, they are directly shimming to a library, Bgfx is the library Native uses to handle graphics. See BabylonNative/Components.md at master · BabylonJS/BabylonNative · GitHub
In any case, there is no WebGL backend. While Apple has said WebGL is exempt from its OpenGL is depreciated statement, going directly at Metal or having Vulcan available is probably better. There are multiple versions of BABYLON.Engine, one called native engine which gets used for here. This precludes Three.js or any other framework running in BJS-Native.