I think you would be best off to throw the 24MHz
ref clk as differential, and "throw away the other phase"
at the destination. This, because otherwise you will
push 24MHz common mode toggle onto all the high
speed lines and probably make some contributed DJ.
Whatever comes of the coupling and HF CMRR /
prop delay delta. Might cost you some BER margin
on the lines you care more about.
But with it being twinax the coupling is probably
tiny (other than any longitudinal current). That still
could make an eye picture less pretty, if you bounce
the far end ground with all the displacement current
of the shield driven by the 24MHz single ended.
You might try the differential, then cut & ground
the mate, float the mate, take whatever SI readings
you might be on the hook for later and see if it
matters, if so what's best.