It's been a long time since you posted this question, but i'm running into this problem. My attempt to solve it is using code (which can be runned as tool script if you wish) which will unwrap UV2.
export(float) var lightmap_texel_size = 0.4
var old_mesh = mesh as Mesh
mesh = ArrayMesh.new()
for surface_id in range(old_mesh.get_surface_count()):
var old_mat = old_mesh.surface_get_material(surface_id)
use_in_baked_light = true
I won't consider it to be an answer, but it can be useful for others.