If the specs allow you to NOT install flex between the panels and the transformer, and if the transformer is not to big and noisy, then I think that would be a really cool way to go, with bond bushings at each end of the conduit nipples, and lay-in lugs in the transformer case for the GEC. Remember, the code allows you to connect your derived panel's GEC right to the ground bus of the service panel [250(a)(3)(c)exc.].
