I think there may be several other factors to look at here.
I'll avoid talking about the points sunk into the platform costs and just focus on the weapons and defences.
Taking a good look at the odds involved, the main reason for the disparity is due to the superb warlord void shield invul saves. Take that way and the average damage from the heavy rail cannons goes up to a respectable 108.89.
The mortal wounds from the rail cannons give another 3.89 damage.
Missile pods and burst cannons add about 1.5 damage.
That's 114.33 damage there, not that far from that 125 now.
And what about the range? How do you quantify a weapon which has 5 times the range of another?
What about the seekers on the AX-1-0s? Those will put a one time 28 damage on the warlord, assuming no marker support bumping up the BS.
Additionally, I suspect that this example might be pushing the limits of a D6 system, i.e. Resolution wise you can't have anything worse than a 6+, or better than a 2+. Which usually makes the worst weapon vs the best defence comparisons a bit wonky from a math standpoint.
Saying that, looking from a fluff perspective, if we take the Warhound takedown we see in IA2 as our example of how the weapons should interact, yes, the railcannon stats doesn't seem to be enough.