Isn’t baking the antithesis of transparent objects (especially refractive ones).
Baking by it’s very nature bakes, light, colour, complex mesh data from the current scene into the texture - thereby allowing you to apply this detail as a texture map and hence avoiding having to do it in the application the baked texture is used in.
Transparency on the other hand requires dynamic calculations regarding what is going on in the scene at any given point and so cannot be ‘baked in’.
I believe you can bake some transparency in - in the form of an alpha map - but this will be very basic transparency and will not include refractive contributions like you get in glass and ice.