It is necessary for the opacity texture to be set up correctly, when remeshing models with an input opacity texture, for example, hair cards.
Grayscale RGBA textures are required (compared to simple RGB). This is required for the baker to read the opacity information correctly.
Split your scene into opaque and non-opaque meshes. This will allow for correct baking behavior.
Process the opaque models separately from the Non-opaque models (in InstaLOD Studio this can be done using the Selection Filter or the Mesh Match Rules).
Attention: if the models are not watertight, make sure to enable
Ignore Backfaces
For the opacity to transfer correctly onto the output model, bake the Opacity map in the Texture Output window.