First, let me point out some design ideas that would improve your machine:
You now have (from bottom to top) rail, cart, table, rail, cart, table for XY movement and (back to front) rail, cart spindle.
You'd get a better machine with (bottom to top): rail, cart, table, cart, rail, table and (back to front) cart, rail, spindle.
That setup would give more consistent stiffness.
As for filling, you do mean filling the whole structure?
I'm not sure if that can be done with a frame like this, I think doing that would be easiest and best when the machine is upright.
If I were to make a machine that way, I'd probably use tooling plate and screw that together.
I would not trust welding thin steel to stay straight, but I am a very, very poor welder
As for the filling compound, I would choose a very dry mix, like 3% for sand, or even less for small gravel, but be sure to test mixes!
A very dry mix produces the least amount of heat, reducing the chances of distortion.