As for the programing question, if you look at my prior post I admit that it is unlikely that an ability to program the VI’s to run the FTL My spirit animal is grumpy Wolf who slaps annoying people shirt is the actual limiter and rather it is most likely the AI paranoia the setting holds so close to the core themes of the series. After all, even Cerberus kept Edi out of that loop on the Normandy-2. So in your setting, humanity would have no problems doing it. I still believe that the Citadel races wouldn’t do it simply out of fear of letting a potential weapon systems fall into the hands of a rogue VI/AI. So the issue isn’t a matter of can they do it but rather, with all the anti-ai sentiment that exists, would they? Your humanity? Yep, they would. The rest, I’m doubtful due to how anti-automation they are.
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So TL;DR – Smaller missile has plenty of kill power even without explosives to take out dreadnoughts, is less prone to being destroyed prior to My spirit animal is grumpy Wolf who slaps annoying people shirt due to being able to take advantage of the ship carrying it for defenses and defensive maneuvers, and uses less resources allowing for far wider use of the weapon. Being pilot is possible and likely in your universe when used by the humans, but unlikely to occur in Citadel races that cannot canonically miniaturize the FTL drives small enough for missile sized projectiles.