once you freeze the mesh you basically reorder the points so the transfer attributes wont work in this respect.

However...as this looks like it has been modelled symmetrically, you could try using the transfer vertex order.

So, as a suggestion. mirror a blendshape and freeze its transforms, then use the default model as your source for the vertex order and try transfering the points that way, it may well work, though you'd have to do this for every mirrored shape.

If this fails, there are some mirror blendshape scripts available out there, as Ive used them myself.

also before you use any rig or skeleton setups, always know the basics and any issues that can be caused and get rid of these errors first before plugging it into an auto rig of any kind, because by adding the extra things into the shapes you are giving yourself a minefield of issues to solve the minute it goes tits up. Character setup is NOT as easy as any auto rig plugin suggests - I dont care what anyone says.

I'll rattle my brain a bit more but usually with character work we have a set up where we use the same mesh over and over for any new character so our blendshapes have already been done in alot of respects.

cheers
J