Deviating from this doesn't generally lead to any loss at all, but if one goes far enough with a flat or long capacitor (like 1:50 for a capital nose gun I have) I have found it increasingly difficult to place the spacing appropriately, particularly if the energy density is low (ie. if it isn't made of hafnia) and this can reach a point where the peak discharge starts to decline.
You could try a tandem projectile made of two rods with a spacer between, though this is even more likely to allow massive bugged velocities on the gun. One will crash into the whipple shield and the other through the hole in it, if the simulation is accurate enough.
Well it seems it works. Made a tandem version and it does indeed punch through armor like you suggested. And it only slightly effected the muzzle velocity and range. 132kms and 1.98 Mm
No screen shots atm but I will update this post with them when I get a chance.
What kind of performance do you get if you don't use a payload? I'm pretty sure this is just a glitch related to payload stress forces.