Ok. So this is a yes, and no answer
Yes there is the ability to export the second set of uv’s as a texture uv asset. Sync tool will do that if you tick the “Second UVs” checkbox.
However, to utilize this you will need a shader that is capable of using it. This is one of the reasons a custom shader and render script will need to be provided. The shader will need to utilize the second stream obviously to render the other textures using it. And of course you need texture samples for that new stream in the shader.
It is not difficult to do this right now. You can export with the sync tool, it will generate all the appropriate data and references, you just need to have a shader suited for it and you replace the shader in the material (use the pbr shader) to your custom one.
I have been working on the concept of using the emission texture slot for things like light maps.
As to whether lightmap or dynamic is better, I suspect it will come down to your needs. Lightmaps are great if the lighting is kinda static like in many indoor situations and you can use dynamic in combo with the lightmap to generate a nice look. Or maybe you are doing outdoors and you really only care about dynamic realtime lighting with dynamic shadows… all depends.
With sync tool the aim is to provide a capability for this possible use, but it wont really provide a rendering solution on how that data is used - theres many ways to tackle lighting models.