I think you're overthinking this quote a bit. Bluebell's joke and simile are just based on the fact that the runty Fiver is the last rabbit anyone would expect a bunch of burly Efrafans to surrender to.
Fiver is one of the smallest rabbits in the story, protected by his brother Hazel (ultimately the Chief Rabbit) and his clairvoyance that sometimes enables him to scare other rabbits even without any physical strength. In the last battle with the Efrafans, he plays a big role in the victory by giving Hazel the idea of loosing the farm dog on the enemy. Shortly before the paragraph you quote, he faces down the savage and feared Captain Vervain of the Efrafan Owsla:
Vervain advanced slowly across the floor. Even he could derive little
satisfaction from the prospect of killing a tharn rabbit half his own size, in
obedience to a contemptuous taunt. The small rabbit made no move whatever,
either to retreat or to defend himself, but only stared at him from great eyes
which, though troubled, were certainly not those of a beaten enemy or a victim.
Before his gaze, Vervain stopped in uncertainty and for long moments the two
faced each other in the dim light. Then, very quietly and with no trace of fear, the
strange rabbit said,
"I am sorry for you with all my heart. But you cannot blame us, for you came to
kill us if you could."
"Blame you?" answered Vervain. "Blame you for what?"
"For your death. Believe me, I am sorry for your death."
Vervain in his time had encountered any number of prisoners who, before they
died, had cursed or threatened him, not uncommonly with supernatural
vengeance, much as Bigwig had cursed Woundwort in the storm. If such things
had been liable to have any effect on him, he would not have been head of the
Owslafa. Indeed, for almost any utterance that a rabbit in this dreadful situation
could find to make, Vervain was unthinkingly ready with one or other of a stock
of jeering rejoinders. Now, as he continued to meet the eyes of this unaccountable
enemy -- the only one he had faced in all the long night's search for bloodshed --
horror came upon him and he was filled with a sudden fear of his words, gentle
and inexorable as the falling of bitter snow in a land without refuge. The shadowy
recesses of the strange burrow seemed full of whispering, malignant ghosts and
he recognized the forgotten voices of rabbits done to death months since in the
ditches of Efrafa.
"Let me alone!" cried Vervain. "Let me go! Let me go!"
But it was not Fiver's clairvoyance and mystic strength of character that made the five Efrafans surrender to him. When the dog came and scattered the Efrafan crowd, these five entered the Watership Down warren to preserve their lives, and surrendered to the first rabbit they met. They knew the battle was over, they'd lost, and they just wanted to surrender and escape alive. It so happens that Fiver was the only one of the Watership Down rabbits present in the Honeycomb, so it was him that they surrended to.
Only Groundsel, Thistle and three others had the presence of mind to dart
down the opened run when the dog came. Back in the Honeycomb, Groundsel
immediately surrendered himself and his fugitives to Fiver, who was still
bemused from his long trance, and scarcely restored to his senses sufficiently to
grasp what was toward. At length, however, after the five Efrafans had remained
crouching for some time in the burrow, listening to the sounds of the dog hunting
above, Fiver recovered himself, made his way to the mouth of the run where
Bigwig still lay half conscious, and succeeded in making Holly and Silver
understand that the siege was ended.
It's ironic that, of all the rabbits to accept the surrender of a bunch of Efrafans including Captain Groundsel, it should be one of the smallest of the Watership Down rabbits. Had they surrended to Bigwig or Holly or Hazel, there would have been less for Bluebell to joke about.
Given Fiver's runtiness, and assuming that the Efrafan rabbits Woundwort brought for the battle were generally big and burly, one can imagine a scene where the guard is much smaller and weaker than his prisoners, which would make for an amusing sight, especially to a serial joker like Bluebell. Imagine a sheep guarding a pack of dogs, or a mouse chasing a gang of cats - that's the kind of thing we're looking at here. The image Bluebell chooses to capture the irony is a tit (a small bird) guarding a clattering of jackdaws (larger birds) which are moulting (presumably the Efrafans look somewhat down in the mouth after their humiliation and fear).
Why is Fiver called "Captain Fiver"? He isn't a captain and wasn't leading any fighting or such.
That's the point: Fiver is the last rabbit they'd expect to be taking the role of guarding prisoners or accepting surrenders. That's what makes it funny, and Bluebell gives him the tongue-in-cheek title of "Captain" to emphasise the point.