Except with the Bentusi, it's always been implied that it's one Bentusi per ship? And what does that say? If it takes so long for drive plasma, or hell, just plasma, to be vented, then why do the Bentusi even bother integrating themselves if it offers no advantages of a large crew or replaces a ship crew?
You've managed to completely screw up the argument by adding bits that were never said.
The Bentusi have managed to create a system in which one person can operate an interstellar starship. This is a significant achievement and far beyond Hiigaraan practice in most respects; even the motherships did not go that far. It is supplemented by automated strikecraft.However
, all systems have tradeoffs. A Bentusi ship is, for example, armed with only a single offensive and defensive weapon, a triple ion cannon on a semiflexible mount. This makes a great deal of sense, considering it has literally only one person aboard; it cannot engage multiple targets as easily and flexibly as a system which incorporates multiple people.
Similarly, the Naar Directive requires the completion of several complex tasks at once, involving identifying a strike location, rerouting drive plasma, and sealing the effected area off, any one of which could fully occupy a single mind. It is also something that very few rational people would ever consider necessary to design a system to actually do. (How often exactly do you want to have the ability
to incinerate your own crew? How many accidents do you think it would cause?) The Bentusi system is extremely, incredibly advanced, but it is being faced with a problem it is almost certainly not designed to handle and for which the easiest solution, the use of further people to ease the workload, is not available to the system they have designed.
The Bentusi are not cowards or fools. They have simply been confronted with a problem for which they are not prepared, and the answers to which work against their previous design choices. Fixing the issue will take time, time they (and everyone else) do not appear to have when they make the decision to flee.
More so, the "their ability to carry out the Naar Directive may well be related to their hybrid design and simply not something Bentusi ships are capable of doing." is a load of bull****, considering that a lot of ships can't be infected by the Beast.
I point you to the fact that literally to the end of the game Taiidani ships are vulnerable at all sizes; so are regular kushan navy ships unless they're being controlled by the player.