Is lower defense actually desirable?

Are you sure you didn't bypass any important breakpoints, either offensive or defensive?

My guess would be the lower IV one generated slightly more energy than the other one and was able to successfully fire off an extra hydropump somewhere. Perhaps the bulkier one fainted with wasted energy? Something along those lines but I'm no expert, purely speculation.

Can you check the combat log with raid simulations? I haven't looked much deeper at Pokebattler for raids than using it mostly for general rankings of attackers.

I'm suspect like the others that the lower defense gained enough little extra energy through the fight to fire off its final Hydro Pump earlier and the higher defense fainted with more energy remaining.

It\s a lottery like Crapshoot that is completely dependent on the break points, hps, and energy fill, and left over energy.

1st) You have to be looking at a case where the Defense is different breakpoint wise for that level pokemon to even make a difference (pretty rare)

2nd) You have to be looking at a case where the Lower Defense charges a power move just in time before fainting. VS a case where the higher defense survives longer to get a couple extra quick moves in OR even charges its power move.

Generally speaking the odds of lower defense doing more is smaller than the odds of the higher defense doing more. It will happen but probability is probability

Only for pokemon with plenty of HP to spare (such as vape), certainly not for glass cannons.