I seriously doubt that filling the t-slot channels would help at all. Some 80/20 extrusions have large enough open center sections that might work out for you to fill, but the channels themselves would not help at all with that small flat cross-section. Even filling the center segments would only really help torsional rigidity. Deflection at center span would likely not be much affected.
Aluminum has plenty of strength already, what it lacks is rigidity.
I don't use the stuff for long unsupported free spans the way you might need to for a gantry router, but I have always thought that perhaps simply using a steel truss rod through the length of it to pre-tension and put the member under compression might work very well to solve exactly the problem you are worried about. Something I'll have to try eventually when I come to it. Cheap, easy to do, and very light.
It would be a necessary precursor to filling it with epoxy concrete in any case, as to get any real effect on deflection you would need it in there anyway.