I have tried creating a sky type using a model and scene does not seem to make a
difference, I created my model in the script using the standard format
sky blabla
{
type = <stars.mdl>;
layer = 9;
material = mat_sky;
flags = visible,transparent;
view = CAMERA;
}

It will draw as a scene even without declaring it as scene = on, or in the flags. you can layer the models as well using transparent to view them.
I think the engine just makes models default to a scene when created as a sky.It's a different story for sprites as dome projects it as a sky layer
that curves at the edges, and scene creates a cylinder wrapped around your level. So far that's how it works for me, I'm using the same build so it should be the same for you.