no, you cant. Godot only allows 1 set of vertex colors.
This is of what a Godot mesh is made of:
ARRAYVERTEX = 0 --- Array of vertices.
ARRAYNORMAL = 1 --- Array of normals.
ARRAYTANGENT = 2 --- Array of tangents as an array of floats, 4 floats per tangent.
ARRAYCOLOR = 3 --- Array of colors.
ARRAYTEXUV = 4 --- Array of UV coordinates.
ARRAYTEXUV2 = 5 --- Array of second set of UV coordinates.
ARRAYBONES = 6 --- Array of bone data.
ARRAYWEIGHTS = 7 --- Array of weights.
ARRAY_INDEX = 8 --- Array of indices.
you see ... two sets of uv data only one color
And no, you cant change or customize that, its a core component of the engine.
You can allways store additional data into textures. Blender also can bake into textures, so maybe this is your way to go.