Apart from stiffness there is dampening of vibrations to consider. Not fully welding may worsen things there. I have never seen commercial mill or cnc spot welded, that should be enough answer for you.

Not every one uses epoxy. I believe it helps dampening. There is German company selling something similar, it was called Moglis, I am not sure. Will search, I had the link somewhere. It's meant to be used for shimming the rails. You can do that with normal epoxy, though the proper one has high compression rating without deformation.
Shimming definitely will be cheaper. But then you will need long straight edge.