If you use your own shaders then you can set which texture uses which UV coordinates. No problem. You can have multiple UV coords for other effects (decals, wave effects,lookups) etc but only in shaders.
As Blendman says, with the built in stock diffuse texture uses Stage 0 and UV0 and the Lightmap uses Stage 2 and UV1 if they are included in the model file otherwise it uses UV0 coords (same a s diffuse).
It wouldnt make sense to add a UV selection per stage as AppGameKit wouldnt know what to do with each texture stage. It wouldnt know how to blend the textures as there are MANY possible ways of combining the textures and infinate numbers of possibilities. This is why shaders are used these days instead of the older fixed function rendering pipelines of DX8/9. In the vertex and pixel shaders you are in full control of blending textures together, apply effects, normal maps, bump maps, decals, lightmapping etc....
Blender uses a raytracer to produce its images (Blender Render or cycles typically) so the render in AppGameKit using Open GL will never be EXACTLY the same as AppGameKit uses open GL in real time. At least it wont without using custom shaders to add all of the rendering features used in the blender render (such as cook torrence specular).
The lightmap is an overlay and should only darken the lighting from a set level. You have to remember to turn off the SUN lighting and ambient which is on by default and disable lights if your using lightmapping in AppGameKit or the scene looks too bright as your adding light to light thats already baked into the scene. Careful use of the object diffuse and emmisive colors gets a better result too.
AGK doenst have specular built in as a function we can use but specular can be added into a shader fairly easily, its not hard to add a phong shader to do this as I have done it. Ive not got a cook torrence one that will include the lightmap and diffuse in it but I could work on one if I ever get some time so that the scene in AppGameKit would look very similar to the blender render. Its already not far off looking good and its real time dynamic rendering. Just light mapping and bump mapping together looks great and creates quite realistic scenes.
If we could add some PBR rendering too it will look pretty great and still run fast. Its all about using the shaders these days rather then some stcok off the shelf architecture.
EDITED: as my spelling and grammar is ****
