For HVD vs Railgun, it should be pretty straightforward to put some Railguns on the medium ballistics and HVDs on the medium hybrids, and then do a side-by-side comparison of their total damage via the Detailed Combat Results mod.
Are you saying to test them by having a split loadout on one same ship? Because that seems like a flawed testing methodology. The AI is going to behave differently due to the range mismatch. If the AI hangs back at 1000 range to use HVDs, that will obviously make railguns perform worse.
The question should really be if the AI and ship can make up for the range difference with speed/positioning, but the AI won't necessarily try to do that if it still has HVDs.
Obviously the single ship approach has the advantage of ensuring the general battle situation is consistent (so you don't have one ship chase after a frigate and do nothing, ruining the comparison), but IMO, it's better to achieve that by having multiple ships with each loadout, and by averaging over multiple battles, which should theoretically converge to a representative value with enough samples. Whereas testing a mixed loadout is introducing a bias to your results (due to AI behavior) that cannot be averaged out.